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root/group/trunk/OOPSE/libmdtools/SimSetup.cpp

Comparing trunk/OOPSE/libmdtools/SimSetup.cpp (file contents):
Revision 394 by gezelter, Mon Mar 24 21:55:34 2003 UTC vs.
Revision 1139 by gezelter, Wed Apr 28 22:06:29 2004 UTC

#	Line 1 | Line 1
1	<	#include <cstdlib>
1	>	#include <algorithm>
2	>	#include <stdlib.h>
3		#include <iostream>
4	<	#include <cmath>
5	<
4	>	#include <math.h>
5	>	#include <string>
6	>	#include <sprng.h>
7		#include "SimSetup.hpp"
8	+	#include "ReadWrite.hpp"
9		#include "parse_me.h"
10		#include "Integrator.hpp"
11		#include "simError.h"
12	+	#include "RigidBody.hpp"
13	+	//#include "ConjugateMinimizer.hpp"
14	+	#include "OOPSEMinimizer.hpp"
15
16		#ifdef IS_MPI
17		#include "mpiBASS.h"
18		#include "mpiSimulation.hpp"
19		#endif
20
21	+	// some defines for ensemble and Forcefield  cases
22	+
23	+	#define NVE_ENS        0
24	+	#define NVT_ENS        1
25	+	#define NPTi_ENS       2
26	+	#define NPTf_ENS       3
27	+	#define NPTxyz_ENS     4
28	+
29	+
30	+	#define FF_DUFF  0
31	+	#define FF_LJ    1
32	+	#define FF_EAM   2
33	+	#define FF_H2O   3
34	+
35	+	using namespace std;
36	+
37	+	/**
38	+	* Check whether dividend is divisble by divisor or not
39	+	*/
40	+	bool isDivisible(double dividend, double divisor){
41	+	double tolerance = 0.000001;
42	+	double quotient;
43	+	double diff;
44	+	int intQuotient;
45	+
46	+	quotient = dividend / divisor;
47	+
48	+	if (quotient < 0)
49	+	quotient = -quotient;
50	+
51	+	intQuotient = int (quotient + tolerance);
52	+
53	+	diff = fabs(fabs(dividend) - intQuotient  * fabs(divisor));
54	+
55	+	if (diff <= tolerance)
56	+	return true;
57	+	else
58	+	return false;
59	+	}
60	+
61		SimSetup::SimSetup(){
62	+
63	+	initSuspend = false;
64	+	isInfoArray = 0;
65	+	nInfo = 1;
66	+
67		stamps = new MakeStamps();
68		globals = new Globals();
69	<
69	>
70	>
71		#ifdef IS_MPI
72	<	strcpy( checkPointMsg, "SimSetup creation successful" );
72	>	strcpy(checkPointMsg, "SimSetup creation successful");
73		MPIcheckPoint();
74		#endif // IS_MPI
75		}
#	Line 27 | Line 79 | SimSetup::~SimSetup(){
79		delete globals;
80		}
81
82	<	void SimSetup::parseFile( char* fileName ){
82	>	void SimSetup::setSimInfo(SimInfo* the_info, int theNinfo){
83	>	info = the_info;
84	>	nInfo = theNinfo;
85	>	isInfoArray = 1;
86	>	initSuspend = true;
87	>	}
88
89	+
90	+	void SimSetup::parseFile(char* fileName){
91		#ifdef IS_MPI
92	<	if( worldRank == 0 ){
92	>	if (worldRank == 0){
93		#endif // is_mpi
94	<
94	>
95		inFileName = fileName;
96	<	set_interface_stamps( stamps, globals );
97	<
96	>	set_interface_stamps(stamps, globals);
97	>
98		#ifdef IS_MPI
99		mpiEventInit();
100		#endif
101
102	<	yacc_BASS( fileName );
102	>	yacc_BASS(fileName);
103
104		#ifdef IS_MPI
105		throwMPIEvent(NULL);
106		}
107	<	else receiveParse();
107	>	else{
108	>	receiveParse();
109	>	}
110		#endif
111
112		}
113
114		#ifdef IS_MPI
115		void SimSetup::receiveParse(void){
116	<
117	<	set_interface_stamps( stamps, globals );
118	<	mpiEventInit();
119	<	MPIcheckPoint();
59	<	mpiEventLoop();
60	<
116	>	set_interface_stamps(stamps, globals);
117	>	mpiEventInit();
118	>	MPIcheckPoint();
119	>	mpiEventLoop();
120		}
121
122		#endif // is_mpi
123
124	<	void SimSetup::createSim( void ){
124	>	void SimSetup::createSim(void){
125
126	<	MakeStamps *the_stamps;
68	<	Globals* the_globals;
69	<	int i, j;
126	>	// gather all of the information from the Bass file
127
128	<	// get the stamps and globals;
72	<	the_stamps = stamps;
73	<	the_globals = globals;
128	>	gatherInfo();
129
130	<	// set the easy ones first
76	<	simnfo->target_temp = the_globals->getTargetTemp();
77	<	simnfo->dt = the_globals->getDt();
78	<	simnfo->run_time = the_globals->getRunTime();
130	>	// creation of complex system objects
131
132	<	// get the ones we know are there, yet still may need some work.
81	<	n_components = the_globals->getNComponents();
82	<	strcpy( force_field, the_globals->getForceField() );
83	<	strcpy( ensemble, the_globals->getEnsemble() );
84	<	strcpy( simnfo->ensemble, ensemble );
132	>	sysObjectsCreation();
133
134	<	strcpy( simnfo->mixingRule, the_globals->getMixingRule() );
87	<	simnfo->usePBC = the_globals->getPBC();
88	<
134	>	// check on the post processing info
135
136	+	finalInfoCheck();
137
138	<	if( !strcmp( force_field, "TraPPE" ) ) the_ff = new TraPPEFF();
92	<	else if( !strcmp( force_field, "DipoleTest" ) ) the_ff = new DipoleTestFF();
93	<	else if( !strcmp( force_field, "TraPPE_Ex" ) ) the_ff = new TraPPE_ExFF();
94	<	else if( !strcmp( force_field, "LJ" ) ) the_ff = new LJ_FF();
95	<	else{
96	<	sprintf( painCave.errMsg,
97	<	"SimSetup Error. Unrecognized force field -> %s\n",
98	<	force_field );
99	<	painCave.isFatal = 1;
100	<	simError();
101	<	}
138	>	// initialize the system coordinates
139
140	<	#ifdef IS_MPI
141	<	strcpy( checkPointMsg, "ForceField creation successful" );
105	<	MPIcheckPoint();
106	<	#endif // is_mpi
140	>	if ( !initSuspend ){
141	>	initSystemCoords();
142
143	+	if( !(globals->getUseInitTime()) )
144	+	info[0].currentTime = 0.0;
145	+	}
146	+
147	+	// make the output filenames
148	+
149	+	makeOutNames();
150
151	+	#ifdef IS_MPI
152	+	mpiSim->mpiRefresh();
153	+	#endif
154
155	<	// get the components and calculate the tot_nMol and indvidual n_mol
111	<	the_components = the_globals->getComponents();
112	<	components_nmol = new int[n_components];
113	<	comp_stamps = new MoleculeStamp*[n_components];
155	>	// initialize the Fortran
156
157	<	if( !the_globals->haveNMol() ){
116	<	// we don't have the total number of molecules, so we assume it is
117	<	// given in each component
157	>	initFortran();
158
159	<	tot_nmol = 0;
160	<	for( i=0; i<n_components; i++ ){
159	>	if (globals->haveMinimizer())
160	>	// make minimizer
161	>	makeMinimizer();
162	>	else
163	>	// make the integrator
164	>	makeIntegrator();
165
166	<	if( !the_components[i]->haveNMol() ){
123	<	// we have a problem
124	<	sprintf( painCave.errMsg,
125	<	"SimSetup Error. No global NMol or component NMol"
126	<	" given. Cannot calculate the number of atoms.\n" );
127	<	painCave.isFatal = 1;
128	<	simError();
129	<	}
166	>	}
167
131	–	tot_nmol += the_components[i]->getNMol();
132	–	components_nmol[i] = the_components[i]->getNMol();
133	–	}
134	–	}
135	–	else{
136	–	sprintf( painCave.errMsg,
137	–	"SimSetup error.\n"
138	–	"\tSorry, the ability to specify total"
139	–	" nMols and then give molfractions in the components\n"
140	–	"\tis not currently supported."
141	–	" Please give nMol in the components.\n" );
142	–	painCave.isFatal = 1;
143	–	simError();
144	–
145	–
146	–	//     tot_nmol = the_globals->getNMol();
147	–
148	–	//   //we have the total number of molecules, now we check for molfractions
149	–	//     for( i=0; i<n_components; i++ ){
150	–
151	–	//       if( !the_components[i]->haveMolFraction() ){
152	–
153	–	//  if( !the_components[i]->haveNMol() ){
154	–	//    //we have a problem
155	–	//    std::cerr << "SimSetup error. Neither molFraction nor "
156	–	//              << " nMol was given in component
157	–
158	–	}
168
169	<	#ifdef IS_MPI
170	<	strcpy( checkPointMsg, "Have the number of components" );
171	<	MPIcheckPoint();
172	<	#endif // is_mpi
169	>	void SimSetup::makeMolecules(void){
170	>	int i, j, k;
171	>	int exI, exJ, exK, exL, slI, slJ;
172	>	int tempI, tempJ, tempK, tempL;
173	>	int molI;
174	>	int stampID, atomOffset, rbOffset;
175	>	molInit molInfo;
176	>	DirectionalAtom* dAtom;
177	>	RigidBody* myRB;
178	>	StuntDouble* mySD;
179	>	LinkedAssign* extras;
180	>	LinkedAssign* current_extra;
181	>	AtomStamp* currentAtom;
182	>	BondStamp* currentBond;
183	>	BendStamp* currentBend;
184	>	TorsionStamp* currentTorsion;
185	>	RigidBodyStamp* currentRigidBody;
186
187	<	// make an array of molecule stamps that match the components used.
188	<	// also extract the used stamps out into a separate linked list
187	>	bond_pair* theBonds;
188	>	bend_set* theBends;
189	>	torsion_set* theTorsions;
190
191	<	simnfo->nComponents = n_components;
169	<	simnfo->componentsNmol = components_nmol;
170	<	simnfo->compStamps = comp_stamps;
171	<	simnfo->headStamp = new LinkedMolStamp();
172	<
173	<	char* id;
174	<	LinkedMolStamp* headStamp = simnfo->headStamp;
175	<	LinkedMolStamp* currentStamp = NULL;
176	<	for( i=0; i<n_components; i++ ){
191	>	set<int> skipList;
192
193	<	id = the_components[i]->getType();
194	<	comp_stamps[i] = NULL;
195	<
181	<	// check to make sure the component isn't already in the list
193	>	double phi, theta, psi;
194	>	char* molName;
195	>	char rbName[100];
196
197	<	comp_stamps[i] = headStamp->match( id );
184	<	if( comp_stamps[i] == NULL ){
185	<
186	<	// extract the component from the list;
187	<
188	<	currentStamp = the_stamps->extractMolStamp( id );
189	<	if( currentStamp == NULL ){
190	<	sprintf( painCave.errMsg,
191	<	"SimSetup error: Component \"%s\" was not found in the "
192	<	"list of declared molecules\n",
193	<	id );
194	<	painCave.isFatal = 1;
195	<	simError();
196	<	}
197	<
198	<	headStamp->add( currentStamp );
199	<	comp_stamps[i] = headStamp->match( id );
200	<	}
201	<	}
197	>	//init the forceField paramters
198
199	<	#ifdef IS_MPI
204	<	strcpy( checkPointMsg, "Component stamps successfully extracted\n" );
205	<	MPIcheckPoint();
206	<	#endif // is_mpi
207	<
199	>	the_ff->readParams();
200
201	+	// init the atoms
202
203	+	int nMembers, nNew, rb1, rb2;
204
205	<	// caclulate the number of atoms, bonds, bends and torsions
205	>	for (k = 0; k < nInfo; k++){
206	>	the_ff->setSimInfo(&(info[k]));
207
208	<	tot_atoms = 0;
214	<	tot_bonds = 0;
215	<	tot_bends = 0;
216	<	tot_torsions = 0;
217	<	for( i=0; i<n_components; i++ ){
218	<
219	<	tot_atoms +=    components_nmol[i] * comp_stamps[i]->getNAtoms();
220	<	tot_bonds +=    components_nmol[i] * comp_stamps[i]->getNBonds();
221	<	tot_bends +=    components_nmol[i] * comp_stamps[i]->getNBends();
222	<	tot_torsions += components_nmol[i] * comp_stamps[i]->getNTorsions();
223	<	}
208	>	atomOffset = 0;
209
210	<	tot_SRI = tot_bonds + tot_bends + tot_torsions;
210	>	for (i = 0; i < info[k].n_mol; i++){
211	>	stampID = info[k].molecules[i].getStampID();
212	>	molName = comp_stamps[stampID]->getID();
213
214	<	simnfo->n_atoms = tot_atoms;
215	<	simnfo->n_bonds = tot_bonds;
216	<	simnfo->n_bends = tot_bends;
217	<	simnfo->n_torsions = tot_torsions;
218	<	simnfo->n_SRI = tot_SRI;
219	<	simnfo->n_mol = tot_nmol;
214	>	molInfo.nAtoms = comp_stamps[stampID]->getNAtoms();
215	>	molInfo.nBonds = comp_stamps[stampID]->getNBonds();
216	>	molInfo.nBends = comp_stamps[stampID]->getNBends();
217	>	molInfo.nTorsions = comp_stamps[stampID]->getNTorsions();
218	>	molInfo.nRigidBodies = comp_stamps[stampID]->getNRigidBodies();
219	>
220	>	molInfo.myAtoms = &(info[k].atoms[atomOffset]);
221
222	<
223	<	#ifdef IS_MPI
222	>	if (molInfo.nBonds > 0)
223	>	molInfo.myBonds = new (Bond *) [molInfo.nBonds];
224	>	else
225	>	molInfo.myBonds = NULL;
226
227	<	// divide the molecules among processors here.
228	<
229	<	mpiSim = new mpiSimulation( simnfo );
230	<
241	<
227	>	if (molInfo.nBends > 0)
228	>	molInfo.myBends = new (Bend *) [molInfo.nBends];
229	>	else
230	>	molInfo.myBends = NULL;
231
232	<	globalIndex = mpiSim->divideLabor();
232	>	if (molInfo.nTorsions > 0)
233	>	molInfo.myTorsions = new (Torsion *) [molInfo.nTorsions];
234	>	else
235	>	molInfo.myTorsions = NULL;
236
237	<
238	<
239	<	// set up the local variables
248	<
249	<	int localMol, allMol;
250	<	int local_atoms, local_bonds, local_bends, local_torsions, local_SRI;
251	<
252	<	allMol = 0;
253	<	localMol = 0;
254	<	local_atoms = 0;
255	<	local_bonds = 0;
256	<	local_bends = 0;
257	<	local_torsions = 0;
258	<	for( i=0; i<n_components; i++ ){
259	<
260	<	for( j=0; j<components_nmol[i]; j++ ){
237	>	theBonds = new bond_pair[molInfo.nBonds];
238	>	theBends = new bend_set[molInfo.nBends];
239	>	theTorsions = new torsion_set[molInfo.nTorsions];
240
241	<	if( mpiSim->getMyMolStart() <= allMol &&
263	<	allMol <= mpiSim->getMyMolEnd() ){
264	<
265	<	local_atoms +=    comp_stamps[i]->getNAtoms();
266	<	local_bonds +=    comp_stamps[i]->getNBonds();
267	<	local_bends +=    comp_stamps[i]->getNBends();
268	<	local_torsions += comp_stamps[i]->getNTorsions();
269	<	localMol++;
270	<	}
271	<	allMol++;
272	<	}
273	<	}
274	<	local_SRI = local_bonds + local_bends + local_torsions;
275	<
241	>	// make the Atoms
242
243	<	simnfo->n_atoms = mpiSim->getMyNlocal();
244	<
279	<	if( local_atoms != simnfo->n_atoms ){
280	<	sprintf( painCave.errMsg,
281	<	"SimSetup error: mpiSim's localAtom (%d) and SimSetup's"
282	<	" localAtom (%d) are note equal.\n",
283	<	simnfo->n_atoms,
284	<	local_atoms );
285	<	painCave.isFatal = 1;
286	<	simError();
287	<	}
243	>	for (j = 0; j < molInfo.nAtoms; j++){
244	>	currentAtom = comp_stamps[stampID]->getAtom(j);
245
246	<	simnfo->n_bonds = local_bonds;
247	<	simnfo->n_bends = local_bends;
248	<	simnfo->n_torsions = local_torsions;
249	<	simnfo->n_SRI = local_SRI;
250	<	simnfo->n_mol = localMol;
246	>	if (currentAtom->haveOrientation()){
247	>	dAtom = new DirectionalAtom((j + atomOffset),
248	>	info[k].getConfiguration());
249	>	info[k].n_oriented++;
250	>	molInfo.myAtoms[j] = dAtom;
251
252	<	strcpy( checkPointMsg, "Passed nlocal consistency check." );
253	<	MPIcheckPoint();
254	<
298	<
299	<	#endif // is_mpi
300	<
252	>	// Directional Atoms have standard unit vectors which are oriented
253	>	// in space using the three Euler angles.  We assume the standard
254	>	// unit vector was originally along the z axis below.
255
256	<	// create the atom and short range interaction arrays
256	>	phi = currentAtom->getEulerPhi() * M_PI / 180.0;
257	>	theta = currentAtom->getEulerTheta() * M_PI / 180.0;
258	>	psi = currentAtom->getEulerPsi()* M_PI / 180.0;
259
260	<	Atom::createArrays(simnfo->n_atoms);
261	<	the_atoms = new Atom*[simnfo->n_atoms];
262	<	the_molecules = new Molecule[simnfo->n_mol];
260	>	dAtom->setUnitFrameFromEuler(phi, theta, psi);
261	>
262	>	}
263	>	else{
264
265	+	molInfo.myAtoms[j] = new Atom((j + atomOffset), info[k].getConfiguration());
266
267	<	if( simnfo->n_SRI ){
310	<	the_sris = new SRI*[simnfo->n_SRI];
311	<	the_excludes = new int[2 * simnfo->n_SRI];
312	<	simnfo->globalExcludes = new int;
313	<	simnfo->n_exclude = tot_SRI;
314	<	}
315	<	else{
316	<
317	<	the_excludes = new int[2];
318	<	the_excludes[0] = 0;
319	<	the_excludes[1] = 0;
320	<	simnfo->globalExcludes = new int;
321	<	simnfo->globalExcludes[0] = 0;
267	>	}
268
269	<	simnfo->n_exclude = 1;
270	<	}
269	>	molInfo.myAtoms[j]->setType(currentAtom->getType());
270	>	#ifdef IS_MPI
271
272	<	// set the arrays into the SimInfo object
272	>	molInfo.myAtoms[j]->setGlobalIndex(globalAtomIndex[j + atomOffset]);
273
274	<	simnfo->atoms = the_atoms;
275	<	simnfo->sr_interactions = the_sris;
330	<	simnfo->nGlobalExcludes = 0;
331	<	simnfo->excludes = the_excludes;
274	>	#endif // is_mpi
275	>	}
276
277	+	// make the bonds
278	+	for (j = 0; j < molInfo.nBonds; j++){
279	+	currentBond = comp_stamps[stampID]->getBond(j);
280	+	theBonds[j].a = currentBond->getA() + atomOffset;
281	+	theBonds[j].b = currentBond->getB() + atomOffset;
282
283	<	// get some of the tricky things that may still be in the globals
283	>	tempI = theBonds[j].a;
284	>	tempJ = theBonds[j].b;
285
336	–
337	–	if( the_globals->haveBox() ){
338	–	simnfo->box_x = the_globals->getBox();
339	–	simnfo->box_y = the_globals->getBox();
340	–	simnfo->box_z = the_globals->getBox();
341	–	}
342	–	else if( the_globals->haveDensity() ){
343	–
344	–	double vol;
345	–	vol = (double)tot_nmol / the_globals->getDensity();
346	–	simnfo->box_x = pow( vol, ( 1.0 / 3.0 ) );
347	–	simnfo->box_y = simnfo->box_x;
348	–	simnfo->box_z = simnfo->box_x;
349	–	}
350	–	else{
351	–	if( !the_globals->haveBoxX() ){
352	–	sprintf( painCave.errMsg,
353	–	"SimSetup error, no periodic BoxX size given.\n" );
354	–	painCave.isFatal = 1;
355	–	simError();
356	–	}
357	–	simnfo->box_x = the_globals->getBoxX();
358	–
359	–	if( !the_globals->haveBoxY() ){
360	–	sprintf( painCave.errMsg,
361	–	"SimSetup error, no periodic BoxY size given.\n" );
362	–	painCave.isFatal = 1;
363	–	simError();
364	–	}
365	–	simnfo->box_y = the_globals->getBoxY();
366	–
367	–	if( !the_globals->haveBoxZ() ){
368	–	sprintf( painCave.errMsg,
369	–	"SimSetup error, no periodic BoxZ size given.\n" );
370	–	painCave.isFatal = 1;
371	–	simError();
372	–	}
373	–	simnfo->box_z = the_globals->getBoxZ();
374	–	}
375	–
286		#ifdef IS_MPI
287	<	strcpy( checkPointMsg, "Box size set up" );
288	<	MPIcheckPoint();
289	<	#endif // is_mpi
287	>	exI = info[k].atoms[tempI]->getGlobalIndex() + 1;
288	>	exJ = info[k].atoms[tempJ]->getGlobalIndex() + 1;
289	>	#else
290	>	exI = tempI + 1;
291	>	exJ = tempJ + 1;
292	>	#endif
293
294	+	info[k].excludes->addPair(exI, exJ);
295	+	}
296
297	<	// initialize the arrays
297	>	//make the bends
298	>	for (j = 0; j < molInfo.nBends; j++){
299	>	currentBend = comp_stamps[stampID]->getBend(j);
300	>	theBends[j].a = currentBend->getA() + atomOffset;
301	>	theBends[j].b = currentBend->getB() + atomOffset;
302	>	theBends[j].c = currentBend->getC() + atomOffset;
303
304	<	the_ff->setSimInfo( simnfo );
304	>	if (currentBend->haveExtras()){
305	>	extras = currentBend->getExtras();
306	>	current_extra = extras;
307
308	<	makeAtoms();
309	<	simnfo->identArray = new int[simnfo->n_atoms];
310	<	for(i=0; i<simnfo->n_atoms; i++){
311	<	simnfo->identArray[i] = the_atoms[i]->getIdent();
312	<	}
313	<
314	<	if( tot_bonds ){
393	<	makeBonds();
394	<	}
308	>	while (current_extra != NULL){
309	>	if (!strcmp(current_extra->getlhs(), "ghostVectorSource")){
310	>	switch (current_extra->getType()){
311	>	case 0:
312	>	theBends[j].ghost = current_extra->getInt() + atomOffset;
313	>	theBends[j].isGhost = 1;
314	>	break;
315
316	<	if( tot_bends ){
317	<	makeBends();
318	<	}
316	>	case 1:
317	>	theBends[j].ghost = (int) current_extra->getDouble() +
318	>	atomOffset;
319	>	theBends[j].isGhost = 1;
320	>	break;
321
322	<	if( tot_torsions ){
323	<	makeTorsions();
324	<	}
322	>	default:
323	>	sprintf(painCave.errMsg,
324	>	"SimSetup Error: ghostVectorSource was neither a "
325	>	"double nor an int.\n"
326	>	"-->Bend[%d] in %s\n",
327	>	j, comp_stamps[stampID]->getID());
328	>	painCave.isFatal = 1;
329	>	simError();
330	>	}
331	>	}
332	>	else{
333	>	sprintf(painCave.errMsg,
334	>	"SimSetup Error: unhandled bend assignment:\n"
335	>	"    -->%s in Bend[%d] in %s\n",
336	>	current_extra->getlhs(), j, comp_stamps[stampID]->getID());
337	>	painCave.isFatal = 1;
338	>	simError();
339	>	}
340
341	+	current_extra = current_extra->getNext();
342	+	}
343	+	}
344
345	<	if (the_globals->getUseRF() ) {
346	<	simnfo->useReactionField = 1;
347	<
348	<	if( !the_globals->haveECR() ){
349	<	sprintf( painCave.errMsg,
350	<	"SimSetup Warning: using default value of 1/2 the smallest "
351	<	"box length for the electrostaticCutoffRadius.\n"
352	<	"I hope you have a very fast processor!\n");
353	<	painCave.isFatal = 0;
354	<	simError();
355	<	double smallest;
356	<	smallest = simnfo->box_x;
357	<	if (simnfo->box_y <= smallest) smallest = simnfo->box_y;
418	<	if (simnfo->box_z <= smallest) smallest = simnfo->box_z;
419	<	simnfo->ecr = 0.5 * smallest;
420	<	} else {
421	<	simnfo->ecr        = the_globals->getECR();
422	<	}
345	>	if (theBends[j].isGhost) {
346	>
347	>	tempI = theBends[j].a;
348	>	tempJ = theBends[j].b;
349	>
350	>	#ifdef IS_MPI
351	>	exI = info[k].atoms[tempI]->getGlobalIndex() + 1;
352	>	exJ = info[k].atoms[tempJ]->getGlobalIndex() + 1;
353	>	#else
354	>	exI = tempI + 1;
355	>	exJ = tempJ + 1;
356	>	#endif
357	>	info[k].excludes->addPair(exI, exJ);
358
359	<	if( !the_globals->haveEST() ){
425	<	sprintf( painCave.errMsg,
426	<	"SimSetup Warning: using default value of 0.05 * the "
427	<	"electrostaticCutoffRadius for the electrostaticSkinThickness\n"
428	<	);
429	<	painCave.isFatal = 0;
430	<	simError();
431	<	simnfo->est = 0.05 * simnfo->ecr;
432	<	} else {
433	<	simnfo->est        = the_globals->getEST();
434	<	}
435	<
436	<	if(!the_globals->haveDielectric() ){
437	<	sprintf( painCave.errMsg,
438	<	"SimSetup Error: You are trying to use Reaction Field without"
439	<	"setting a dielectric constant!\n"
440	<	);
441	<	painCave.isFatal = 1;
442	<	simError();
443	<	}
444	<	simnfo->dielectric = the_globals->getDielectric();
445	<	} else {
446	<	if (simnfo->n_dipoles) {
447	<
448	<	if( !the_globals->haveECR() ){
449	<	sprintf( painCave.errMsg,
450	<	"SimSetup Warning: using default value of 1/2 the smallest"
451	<	"box length for the electrostaticCutoffRadius.\n"
452	<	"I hope you have a very fast processor!\n");
453	<	painCave.isFatal = 0;
454	<	simError();
455	<	double smallest;
456	<	smallest = simnfo->box_x;
457	<	if (simnfo->box_y <= smallest) smallest = simnfo->box_y;
458	<	if (simnfo->box_z <= smallest) smallest = simnfo->box_z;
459	<	simnfo->ecr = 0.5 * smallest;
460	<	} else {
461	<	simnfo->ecr        = the_globals->getECR();
462	<	}
463	<
464	<	if( !the_globals->haveEST() ){
465	<	sprintf( painCave.errMsg,
466	<	"SimSetup Warning: using default value of 5% of the"
467	<	"electrostaticCutoffRadius for the "
468	<	"electrostaticSkinThickness\n"
469	<	);
470	<	painCave.isFatal = 0;
471	<	simError();
472	<	simnfo->est = 0.05 * simnfo->ecr;
473	<	} else {
474	<	simnfo->est        = the_globals->getEST();
475	<	}
476	<	}
477	<	}
359	>	} else {
360
361	+	tempI = theBends[j].a;
362	+	tempJ = theBends[j].b;
363	+	tempK = theBends[j].c;
364	+
365		#ifdef IS_MPI
366	<	strcpy( checkPointMsg, "electrostatic parameters check out" );
367	<	MPIcheckPoint();
368	<	#endif // is_mpi
366	>	exI = info[k].atoms[tempI]->getGlobalIndex() + 1;
367	>	exJ = info[k].atoms[tempJ]->getGlobalIndex() + 1;
368	>	exK = info[k].atoms[tempK]->getGlobalIndex() + 1;
369	>	#else
370	>	exI = tempI + 1;
371	>	exJ = tempJ + 1;
372	>	exK = tempK + 1;
373	>	#endif
374	>
375	>	info[k].excludes->addPair(exI, exK);
376	>	info[k].excludes->addPair(exI, exJ);
377	>	info[k].excludes->addPair(exJ, exK);
378	>	}
379	>	}
380
381	<	if( the_globals->haveInitialConfig() ){
382	<
383	<	InitializeFromFile* fileInit;
384	<	#ifdef IS_MPI // is_mpi
385	<	if( worldRank == 0 ){
386	<	#endif //is_mpi
387	<	fileInit = new InitializeFromFile( the_globals->getInitialConfig() );
381	>	for (j = 0; j < molInfo.nTorsions; j++){
382	>	currentTorsion = comp_stamps[stampID]->getTorsion(j);
383	>	theTorsions[j].a = currentTorsion->getA() + atomOffset;
384	>	theTorsions[j].b = currentTorsion->getB() + atomOffset;
385	>	theTorsions[j].c = currentTorsion->getC() + atomOffset;
386	>	theTorsions[j].d = currentTorsion->getD() + atomOffset;
387	>
388	>	tempI = theTorsions[j].a;
389	>	tempJ = theTorsions[j].b;
390	>	tempK = theTorsions[j].c;
391	>	tempL = theTorsions[j].d;
392	>
393		#ifdef IS_MPI
394	<	}else fileInit = new InitializeFromFile( NULL );
394	>	exI = info[k].atoms[tempI]->getGlobalIndex() + 1;
395	>	exJ = info[k].atoms[tempJ]->getGlobalIndex() + 1;
396	>	exK = info[k].atoms[tempK]->getGlobalIndex() + 1;
397	>	exL = info[k].atoms[tempL]->getGlobalIndex() + 1;
398	>	#else
399	>	exI = tempI + 1;
400	>	exJ = tempJ + 1;
401	>	exK = tempK + 1;
402	>	exL = tempL + 1;
403		#endif
494	–	fileInit->read_xyz( simnfo ); // default velocities on
404
405	<	delete fileInit;
406	<	}
407	<	else{
405	>	info[k].excludes->addPair(exI, exJ);
406	>	info[k].excludes->addPair(exI, exK);
407	>	info[k].excludes->addPair(exI, exL);
408	>	info[k].excludes->addPair(exJ, exK);
409	>	info[k].excludes->addPair(exJ, exL);
410	>	info[k].excludes->addPair(exK, exL);
411	>	}
412
413	<	#ifdef IS_MPI
413	>
414	>	molInfo.myRigidBodies.clear();
415	>
416	>	for (j = 0; j < molInfo.nRigidBodies; j++){
417
418	<	// no init from bass
419	<
504	<	sprintf( painCave.errMsg,
505	<	"Cannot intialize a parallel simulation without an initial configuration file.\n" );
506	<	painCave.isFatal;
507	<	simError();
508	<
509	<	#else
418	>	currentRigidBody = comp_stamps[stampID]->getRigidBody(j);
419	>	nMembers = currentRigidBody->getNMembers();
420
421	<	initFromBass();
421	>	// Create the Rigid Body:
422
423	+	myRB = new RigidBody();
424
425	+	sprintf(rbName,"%s_RB_%d", molName, j);
426	+	myRB->setType(rbName);
427	+
428	+	for (rb1 = 0; rb1 < nMembers; rb1++) {
429	+
430	+	// molI is atom numbering inside this molecule
431	+	molI = currentRigidBody->getMember(rb1);
432	+
433	+	// tempI is atom numbering on local processor
434	+	tempI = molI + atomOffset;
435	+
436	+	// currentAtom is the AtomStamp (which we need for
437	+	// rigid body reference positions)
438	+	currentAtom = comp_stamps[stampID]->getAtom(molI);
439	+
440	+	// When we add to the rigid body, add the atom itself and
441	+	// the stamp info:
442	+
443	+	myRB->addAtom(info[k].atoms[tempI], currentAtom);
444	+
445	+	// Add this atom to the Skip List for the integrators
446	+	#ifdef IS_MPI
447	+	slI = info[k].atoms[tempI]->getGlobalIndex();
448	+	#else
449	+	slI = tempI;
450		#endif
451	<	}
451	>	skipList.insert(slI);
452	>
453	>	}
454	>
455	>	for(rb1 = 0; rb1 < nMembers - 1; rb1++) {
456	>	for(rb2 = rb1+1; rb2 < nMembers; rb2++) {
457	>
458	>	tempI = currentRigidBody->getMember(rb1);
459	>	tempJ = currentRigidBody->getMember(rb2);
460	>
461	>	// Some explanation is required here.
462	>	// Fortran indexing starts at 1, while c indexing starts at 0
463	>	// Also, in parallel computations, the GlobalIndex is
464	>	// used for the exclude list:
465	>
466	>	#ifdef IS_MPI
467	>	exI = molInfo.myAtoms[tempI]->getGlobalIndex() + 1;
468	>	exJ = molInfo.myAtoms[tempJ]->getGlobalIndex() + 1;
469	>	#else
470	>	exI = molInfo.myAtoms[tempI]->getIndex() + 1;
471	>	exJ = molInfo.myAtoms[tempJ]->getIndex() + 1;
472	>	#endif
473	>
474	>	info[k].excludes->addPair(exI, exJ);
475	>
476	>	}
477	>	}
478
479	+	molInfo.myRigidBodies.push_back(myRB);
480	+	info[k].rigidBodies.push_back(myRB);
481	+	}
482	+
483	+
484	+	// After this is all set up, scan through the atoms to
485	+	// see if they can be added to the integrableObjects:
486	+
487	+	molInfo.myIntegrableObjects.clear();
488	+
489	+
490	+	for (j = 0; j < molInfo.nAtoms; j++){
491	+
492		#ifdef IS_MPI
493	<	strcpy( checkPointMsg, "Successfully read in the initial configuration" );
494	<	MPIcheckPoint();
495	<	#endif // is_mpi
493	>	slJ = molInfo.myAtoms[j]->getGlobalIndex();
494	>	#else
495	>	slJ = j+atomOffset;
496	>	#endif
497
498	+	// if they aren't on the skip list, then they can be integrated
499
500	<
501	<
502	<
500	>	if (skipList.find(slJ) == skipList.end()) {
501	>	mySD = (StuntDouble *) molInfo.myAtoms[j];
502	>	info[k].integrableObjects.push_back(mySD);
503	>	molInfo.myIntegrableObjects.push_back(mySD);
504	>	}
505	>	}
506
507	<
508	<	#ifdef IS_MPI
509	<	if( worldRank == 0 ){
510	<	#endif // is_mpi
507	>	// all rigid bodies are integrated:
508	>
509	>	for (j = 0; j < molInfo.nRigidBodies; j++) {
510	>	mySD = (StuntDouble *) molInfo.myRigidBodies[j];
511	>	info[k].integrableObjects.push_back(mySD);
512	>	molInfo.myIntegrableObjects.push_back(mySD);
513	>	}
514
515	<	if( the_globals->haveFinalConfig() ){
516	<	strcpy( simnfo->finalName, the_globals->getFinalConfig() );
517	<	}
518	<	else{
519	<	strcpy( simnfo->finalName, inFileName );
520	<	char* endTest;
521	<	int nameLength = strlen( simnfo->finalName );
522	<	endTest = &(simnfo->finalName[nameLength - 5]);
523	<	if( !strcmp( endTest, ".bass" ) ){
524	<	strcpy( endTest, ".eor" );
525	<	}
526	<	else if( !strcmp( endTest, ".BASS" ) ){
527	<	strcpy( endTest, ".eor" );
528	<	}
529	<	else{
530	<	endTest = &(simnfo->finalName[nameLength - 4]);
531	<	if( !strcmp( endTest, ".bss" ) ){
549	<	strcpy( endTest, ".eor" );
550	<	}
551	<	else if( !strcmp( endTest, ".mdl" ) ){
552	<	strcpy( endTest, ".eor" );
553	<	}
554	<	else{
555	<	strcat( simnfo->finalName, ".eor" );
556	<	}
557	<	}
558	<	}
559	<
560	<	// make the sample and status out names
561	<
562	<	strcpy( simnfo->sampleName, inFileName );
563	<	char* endTest;
564	<	int nameLength = strlen( simnfo->sampleName );
565	<	endTest = &(simnfo->sampleName[nameLength - 5]);
566	<	if( !strcmp( endTest, ".bass" ) ){
567	<	strcpy( endTest, ".dump" );
568	<	}
569	<	else if( !strcmp( endTest, ".BASS" ) ){
570	<	strcpy( endTest, ".dump" );
571	<	}
572	<	else{
573	<	endTest = &(simnfo->sampleName[nameLength - 4]);
574	<	if( !strcmp( endTest, ".bss" ) ){
575	<	strcpy( endTest, ".dump" );
576	<	}
577	<	else if( !strcmp( endTest, ".mdl" ) ){
578	<	strcpy( endTest, ".dump" );
579	<	}
580	<	else{
581	<	strcat( simnfo->sampleName, ".dump" );
582	<	}
583	<	}
584	<
585	<	strcpy( simnfo->statusName, inFileName );
586	<	nameLength = strlen( simnfo->statusName );
587	<	endTest = &(simnfo->statusName[nameLength - 5]);
588	<	if( !strcmp( endTest, ".bass" ) ){
589	<	strcpy( endTest, ".stat" );
590	<	}
591	<	else if( !strcmp( endTest, ".BASS" ) ){
592	<	strcpy( endTest, ".stat" );
593	<	}
594	<	else{
595	<	endTest = &(simnfo->statusName[nameLength - 4]);
596	<	if( !strcmp( endTest, ".bss" ) ){
597	<	strcpy( endTest, ".stat" );
598	<	}
599	<	else if( !strcmp( endTest, ".mdl" ) ){
600	<	strcpy( endTest, ".stat" );
601	<	}
602	<	else{
603	<	strcat( simnfo->statusName, ".stat" );
604	<	}
605	<	}
606	<
607	<	#ifdef IS_MPI
515	>
516	>	// send the arrays off to the forceField for init.
517	>
518	>	the_ff->initializeAtoms(molInfo.nAtoms, molInfo.myAtoms);
519	>	the_ff->initializeBonds(molInfo.nBonds, molInfo.myBonds, theBonds);
520	>	the_ff->initializeBends(molInfo.nBends, molInfo.myBends, theBends);
521	>	the_ff->initializeTorsions(molInfo.nTorsions, molInfo.myTorsions,
522	>	theTorsions);
523	>
524	>	info[k].molecules[i].initialize(molInfo);
525	>
526	>
527	>	atomOffset += molInfo.nAtoms;
528	>	delete[] theBonds;
529	>	delete[] theBends;
530	>	delete[] theTorsions;
531	>	}
532		}
533	+
534	+	#ifdef IS_MPI
535	+	sprintf(checkPointMsg, "all molecules initialized succesfully");
536	+	MPIcheckPoint();
537		#endif // is_mpi
610	–
611	–	// set the status, sample, and themal kick times
612	–
613	–	if( the_globals->haveSampleTime() ){
614	–	simnfo->sampleTime = the_globals->getSampleTime();
615	–	simnfo->statusTime = simnfo->sampleTime;
616	–	simnfo->thermalTime = simnfo->sampleTime;
617	–	}
618	–	else{
619	–	simnfo->sampleTime = the_globals->getRunTime();
620	–	simnfo->statusTime = simnfo->sampleTime;
621	–	simnfo->thermalTime = simnfo->sampleTime;
622	–	}
538
539	<	if( the_globals->haveStatusTime() ){
625	<	simnfo->statusTime = the_globals->getStatusTime();
626	<	}
539	>	// clean up the forcefield
540
541	<	if( the_globals->haveThermalTime() ){
629	<	simnfo->thermalTime = the_globals->getThermalTime();
630	<	}
541	>	if (!globals->haveLJrcut()){
542
543	<	// check for the temperature set flag
543	>	the_ff->calcRcut();
544
545	<	if( the_globals->haveTempSet() ) simnfo->setTemp = the_globals->getTempSet();
545	>	} else {
546	>
547	>	the_ff->setRcut( globals->getLJrcut() );
548	>	}
549
550	+	the_ff->cleanMe();
551	+	}
552
553	<	//   // make the longe range forces and the integrator
553	>	void SimSetup::initFromBass(void){
554	>	int i, j, k;
555	>	int n_cells;
556	>	double cellx, celly, cellz;
557	>	double temp1, temp2, temp3;
558	>	int n_per_extra;
559	>	int n_extra;
560	>	int have_extra, done;
561
562	<	//   new AllLong( simnfo );
562	>	double vel[3];
563	>	vel[0] = 0.0;
564	>	vel[1] = 0.0;
565	>	vel[2] = 0.0;
566
567	<	if( !strcmp( force_field, "TraPPE" ) ) new Verlet( *simnfo, the_ff );
568	<	if( !strcmp( force_field, "DipoleTest" ) ) new Symplectic( simnfo, the_ff );
569	<	if( !strcmp( force_field, "TraPPE_Ex" ) ) new Symplectic( simnfo, the_ff );
644	<	if( !strcmp( force_field, "LJ" ) ) new Verlet( *simnfo, the_ff );
567	>	temp1 = (double) tot_nmol / 4.0;
568	>	temp2 = pow(temp1, (1.0 / 3.0));
569	>	temp3 = ceil(temp2);
570
571	+	have_extra = 0;
572	+	if (temp2 < temp3){
573	+	// we have a non-complete lattice
574	+	have_extra = 1;
575
576	+	n_cells = (int) temp3 - 1;
577	+	cellx = info[0].boxL[0] / temp3;
578	+	celly = info[0].boxL[1] / temp3;
579	+	cellz = info[0].boxL[2] / temp3;
580	+	n_extra = tot_nmol - (4 * n_cells * n_cells * n_cells);
581	+	temp1 = ((double) n_extra) / (pow(temp3, 3.0) - pow(n_cells, 3.0));
582	+	n_per_extra = (int) ceil(temp1);
583
584	<	// initialize the Fortran
585	<
586	<	simnfo->refreshSim();
587	<
588	<	if( !strcmp( simnfo->mixingRule, "standard") ){
589	<	the_ff->initForceField( LB_MIXING_RULE );
584	>	if (n_per_extra > 4){
585	>	sprintf(painCave.errMsg,
586	>	"SimSetup error. There has been an error in constructing"
587	>	" the non-complete lattice.\n");
588	>	painCave.isFatal = 1;
589	>	simError();
590	>	}
591		}
655	–	else if( !strcmp( simnfo->mixingRule, "explicit") ){
656	–	the_ff->initForceField( EXPLICIT_MIXING_RULE );
657	–	}
592		else{
593	<	sprintf( painCave.errMsg,
594	<	"SimSetup Error: unknown mixing rule -> \"%s\"\n",
595	<	simnfo->mixingRule );
596	<	painCave.isFatal = 1;
663	<	simError();
593	>	n_cells = (int) temp3;
594	>	cellx = info[0].boxL[0] / temp3;
595	>	celly = info[0].boxL[1] / temp3;
596	>	cellz = info[0].boxL[2] / temp3;
597		}
598
599	+	current_mol = 0;
600	+	current_comp_mol = 0;
601	+	current_comp = 0;
602	+	current_atom_ndx = 0;
603
604	<	#ifdef IS_MPI
605	<	strcpy( checkPointMsg,
606	<	"Successfully intialized the mixingRule for Fortran." );
607	<	MPIcheckPoint();
671	<	#endif // is_mpi
672	<	}
604	>	for (i = 0; i < n_cells ; i++){
605	>	for (j = 0; j < n_cells; j++){
606	>	for (k = 0; k < n_cells; k++){
607	>	makeElement(i * cellx, j * celly, k * cellz);
608
609	<	void SimSetup::makeAtoms( void ){
609	>	makeElement(i * cellx + 0.5 * cellx, j * celly + 0.5 * celly, k * cellz);
610
611	<	int i, j, k, index;
677	<	double ux, uy, uz, uSqr, u;
678	<	AtomStamp* current_atom;
611	>	makeElement(i * cellx, j * celly + 0.5 * celly, k * cellz + 0.5 * cellz);
612
613	<	DirectionalAtom* dAtom;
614	<	int molIndex, molStart, molEnd, nMemb, lMolIndex;
613	>	makeElement(i * cellx + 0.5 * cellx, j * celly, k * cellz + 0.5 * cellz);
614	>	}
615	>	}
616	>	}
617
618	<	lMolIndex = 0;
619	<	molIndex = 0;
685	<	index = 0;
686	<	for( i=0; i<n_components; i++ ){
618	>	if (have_extra){
619	>	done = 0;
620
621	<	for( j=0; j<components_nmol[i]; j++ ){
622	<
623	<	#ifdef IS_MPI
624	<	if( mpiSim->getMyMolStart() <= molIndex &&
625	<	molIndex <= mpiSim->getMyMolEnd() ){
626	<	#endif // is_mpi
627	<
628	<	molStart = index;
629	<	nMemb = comp_stamps[i]->getNAtoms();
630	<	for( k=0; k<comp_stamps[i]->getNAtoms(); k++ ){
631	<
632	<	current_atom = comp_stamps[i]->getAtom( k );
700	<	if( current_atom->haveOrientation() ){
701	<
702	<	dAtom = new DirectionalAtom(index);
703	<	simnfo->n_oriented++;
704	<	the_atoms[index] = dAtom;
705	<
706	<	ux = current_atom->getOrntX();
707	<	uy = current_atom->getOrntY();
708	<	uz = current_atom->getOrntZ();
709	<
710	<	uSqr = (ux * ux) + (uy * uy) + (uz * uz);
711	<
712	<	u = sqrt( uSqr );
713	<	ux = ux / u;
714	<	uy = uy / u;
715	<	uz = uz / u;
716	<
717	<	dAtom->setSUx( ux );
718	<	dAtom->setSUy( uy );
719	<	dAtom->setSUz( uz );
720	<	}
721	<	else{
722	<	the_atoms[index] = new GeneralAtom(index);
723	<	}
724	<	the_atoms[index]->setType( current_atom->getType() );
725	<	the_atoms[index]->setIndex( index );
726	<
727	<	// increment the index and repeat;
728	<	index++;
729	<	}
730	<
731	<	molEnd = index -1;
732	<	the_molecules[lMolIndex].setNMembers( nMemb );
733	<	the_molecules[lMolIndex].setStartAtom( molStart );
734	<	the_molecules[lMolIndex].setEndAtom( molEnd );
735	<	the_molecules[lMolIndex].setStampID( i );
736	<	lMolIndex++;
621	>	int start_ndx;
622	>	for (i = 0; i < (n_cells + 1) && !done; i++){
623	>	for (j = 0; j < (n_cells + 1) && !done; j++){
624	>	if (i < n_cells){
625	>	if (j < n_cells){
626	>	start_ndx = n_cells;
627	>	}
628	>	else
629	>	start_ndx = 0;
630	>	}
631	>	else
632	>	start_ndx = 0;
633
634	<	#ifdef IS_MPI
634	>	for (k = start_ndx; k < (n_cells + 1) && !done; k++){
635	>	makeElement(i * cellx, j * celly, k * cellz);
636	>	done = (current_mol >= tot_nmol);
637	>
638	>	if (!done && n_per_extra > 1){
639	>	makeElement(i * cellx + 0.5 * cellx, j * celly + 0.5 * celly,
640	>	k * cellz);
641	>	done = (current_mol >= tot_nmol);
642	>	}
643	>
644	>	if (!done && n_per_extra > 2){
645	>	makeElement(i * cellx, j * celly + 0.5 * celly,
646	>	k * cellz + 0.5 * cellz);
647	>	done = (current_mol >= tot_nmol);
648	>	}
649	>
650	>	if (!done && n_per_extra > 3){
651	>	makeElement(i * cellx + 0.5 * cellx, j * celly,
652	>	k * cellz + 0.5 * cellz);
653	>	done = (current_mol >= tot_nmol);
654	>	}
655	>	}
656		}
740	–	#endif //is_mpi
741	–
742	–	molIndex++;
657		}
658		}
659
660	<	#ifdef IS_MPI
661	<	for( i=0; i<mpiSim->getMyNlocal(); i++ ) the_atoms[i]->setGlobalIndex( globalIndex[i] );
662	<
749	<	delete[] globalIndex;
750	<
751	<	mpiSim->mpiRefresh();
752	<	#endif //IS_MPI
753	<
754	<	the_ff->initializeAtoms();
660	>	for (i = 0; i < info[0].n_atoms; i++){
661	>	info[0].atoms[i]->setVel(vel);
662	>	}
663		}
664
665	<	void SimSetup::makeBonds( void ){
665	>	void SimSetup::makeElement(double x, double y, double z){
666	>	int k;
667	>	AtomStamp* current_atom;
668	>	DirectionalAtom* dAtom;
669	>	double rotMat[3][3];
670	>	double pos[3];
671
672	<	int i, j, k, index, offset, molIndex, exI, exJ, tempEx;
673	<	bond_pair* the_bonds;
674	<	BondStamp* current_bond;
672	>	for (k = 0; k < comp_stamps[current_comp]->getNAtoms(); k++){
673	>	current_atom = comp_stamps[current_comp]->getAtom(k);
674	>	if (!current_atom->havePosition()){
675	>	sprintf(painCave.errMsg,
676	>	"SimSetup:initFromBass error.\n"
677	>	"\tComponent %s, atom %s does not have a position specified.\n"
678	>	"\tThe initialization routine is unable to give a start"
679	>	" position.\n",
680	>	comp_stamps[current_comp]->getID(), current_atom->getType());
681	>	painCave.isFatal = 1;
682	>	simError();
683	>	}
684
685	<	the_bonds = new bond_pair[tot_bonds];
686	<	index = 0;
687	<	offset = 0;
766	<	molIndex = 0;
685	>	pos[0] = x + current_atom->getPosX();
686	>	pos[1] = y + current_atom->getPosY();
687	>	pos[2] = z + current_atom->getPosZ();
688
689	<	for( i=0; i<n_components; i++ ){
689	>	info[0].atoms[current_atom_ndx]->setPos(pos);
690
691	<	for( j=0; j<components_nmol[i]; j++ ){
691	>	if (info[0].atoms[current_atom_ndx]->isDirectional()){
692	>	dAtom = (DirectionalAtom *) info[0].atoms[current_atom_ndx];
693
694	<	#ifdef IS_MPI
695	<	if( mpiSim->getMyMolStart() <= molIndex &&
696	<	molIndex <= mpiSim->getMyMolEnd() ){
775	<	#endif // is_mpi
776	<
777	<	for( k=0; k<comp_stamps[i]->getNBonds(); k++ ){
778	<
779	<	current_bond = comp_stamps[i]->getBond( k );
780	<	the_bonds[index].a = current_bond->getA() + offset;
781	<	the_bonds[index].b = current_bond->getB() + offset;
694	>	rotMat[0][0] = 1.0;
695	>	rotMat[0][1] = 0.0;
696	>	rotMat[0][2] = 0.0;
697
698	<	exI = the_bonds[index].a;
699	<	exJ = the_bonds[index].b;
698	>	rotMat[1][0] = 0.0;
699	>	rotMat[1][1] = 1.0;
700	>	rotMat[1][2] = 0.0;
701
702	<	// exclude_I must always be the smaller of the pair
703	<	if( exI > exJ ){
704	<	tempEx = exI;
789	<	exI = exJ;
790	<	exJ = tempEx;
791	<	}
702	>	rotMat[2][0] = 0.0;
703	>	rotMat[2][1] = 0.0;
704	>	rotMat[2][2] = 1.0;
705
706	<
707	<	#ifdef IS_MPI
706	>	dAtom->setA(rotMat);
707	>	}
708
709	<	the_excludes[index*2] =
797	<	the_atoms[exI]->getGlobalIndex() + 1;
798	<	the_excludes[index*2 + 1] =
799	<	the_atoms[exJ]->getGlobalIndex() + 1;
800	<
801	<	#else  // isn't MPI
802	<
803	<	the_excludes[index*2] =     exI + 1;
804	<	the_excludes[index*2 + 1] = exJ + 1;
805	<	// fortran index from 1 (hence the +1 in the indexing)
806	<	#endif  //is_mpi
807	<
808	<	// increment the index and repeat;
809	<	index++;
810	<	}
811	<	offset += comp_stamps[i]->getNAtoms();
812	<
813	<	#ifdef IS_MPI
814	<	}
815	<	#endif //is_mpi
816	<
817	<	molIndex++;
818	<	}
709	>	current_atom_ndx++;
710		}
711
712	<	the_ff->initializeBonds( the_bonds );
712	>	current_mol++;
713	>	current_comp_mol++;
714	>
715	>	if (current_comp_mol >= components_nmol[current_comp]){
716	>	current_comp_mol = 0;
717	>	current_comp++;
718	>	}
719		}
720
824	–	void SimSetup::makeBends( void ){
721
722	<	int i, j, k, index, offset, molIndex, exI, exJ, tempEx;
723	<	bend_set* the_bends;
828	<	BendStamp* current_bend;
829	<	LinkedAssign* extras;
830	<	LinkedAssign* current_extra;
831	<
722	>	void SimSetup::gatherInfo(void){
723	>	int i;
724
725	<	the_bends = new bend_set[tot_bends];
726	<	index = 0;
835	<	offset = 0;
836	<	molIndex = 0;
837	<	for( i=0; i<n_components; i++ ){
725	>	ensembleCase = -1;
726	>	ffCase = -1;
727
728	<	for( j=0; j<components_nmol[i]; j++ ){
728	>	// set the easy ones first
729
730	<	#ifdef IS_MPI
731	<	if( mpiSim->getMyMolStart() <= molIndex &&
732	<	molIndex <= mpiSim->getMyMolEnd() ){
733	<	#endif // is_mpi
730	>	for (i = 0; i < nInfo; i++){
731	>	info[i].target_temp = globals->getTargetTemp();
732	>	info[i].dt = globals->getDt();
733	>	info[i].run_time = globals->getRunTime();
734	>	}
735	>	n_components = globals->getNComponents();
736
737	<	for( k=0; k<comp_stamps[i]->getNBends(); k++ ){
738	<
848	<	current_bend = comp_stamps[i]->getBend( k );
849	<	the_bends[index].a = current_bend->getA() + offset;
850	<	the_bends[index].b = current_bend->getB() + offset;
851	<	the_bends[index].c = current_bend->getC() + offset;
852	<
853	<	if( current_bend->haveExtras() ){
854	<
855	<	extras = current_bend->getExtras();
856	<	current_extra = extras;
857	<
858	<	while( current_extra != NULL ){
859	<	if( !strcmp( current_extra->getlhs(), "ghostVectorSource" )){
860	<
861	<	switch( current_extra->getType() ){
862	<
863	<	case 0:
864	<	the_bends[index].ghost =
865	<	current_extra->getInt() + offset;
866	<	the_bends[index].isGhost = 1;
867	<	break;
868	<
869	<	case 1:
870	<	the_bends[index].ghost =
871	<	(int)current_extra->getDouble() + offset;
872	<	the_bends[index].isGhost = 1;
873	<	break;
874	<
875	<	default:
876	<	sprintf( painCave.errMsg,
877	<	"SimSetup Error: ghostVectorSource was neiter a "
878	<	"double nor an int.\n"
879	<	"-->Bend[%d] in %s\n",
880	<	k, comp_stamps[i]->getID() );
881	<	painCave.isFatal = 1;
882	<	simError();
883	<	}
884	<	}
885	<
886	<	else{
887	<
888	<	sprintf( painCave.errMsg,
889	<	"SimSetup Error: unhandled bend assignment:\n"
890	<	"    -->%s in Bend[%d] in %s\n",
891	<	current_extra->getlhs(),
892	<	k, comp_stamps[i]->getID() );
893	<	painCave.isFatal = 1;
894	<	simError();
895	<	}
896	<
897	<	current_extra = current_extra->getNext();
898	<	}
899	<	}
900	<
901	<	if( !the_bends[index].isGhost ){
902	<
903	<	exI = the_bends[index].a;
904	<	exJ = the_bends[index].c;
905	<	}
906	<	else{
907	<
908	<	exI = the_bends[index].a;
909	<	exJ = the_bends[index].b;
910	<	}
911	<
912	<	// exclude_I must always be the smaller of the pair
913	<	if( exI > exJ ){
914	<	tempEx = exI;
915	<	exI = exJ;
916	<	exJ = tempEx;
917	<	}
737	>
738	>	// get the forceField
739
740	+	strcpy(force_field, globals->getForceField());
741
742	<	#ifdef IS_MPI
743	<
922	<	the_excludes[(index + tot_bonds)*2] =
923	<	the_atoms[exI]->getGlobalIndex() + 1;
924	<	the_excludes[(index + tot_bonds)*2 + 1] =
925	<	the_atoms[exJ]->getGlobalIndex() + 1;
926	<
927	<	#else  // isn't MPI
928	<
929	<	the_excludes[(index + tot_bonds)*2] =     exI + 1;
930	<	the_excludes[(index + tot_bonds)*2 + 1] = exJ + 1;
931	<	// fortran index from 1 (hence the +1 in the indexing)
932	<	#endif  //is_mpi
933	<
934	<
935	<	// increment the index and repeat;
936	<	index++;
937	<	}
938	<	offset += comp_stamps[i]->getNAtoms();
939	<
940	<	#ifdef IS_MPI
941	<	}
942	<	#endif //is_mpi
943	<
944	<	molIndex++;
945	<	}
742	>	if (!strcasecmp(force_field, "DUFF")){
743	>	ffCase = FF_DUFF;
744		}
745	+	else if (!strcasecmp(force_field, "LJ")){
746	+	ffCase = FF_LJ;
747	+	}
748	+	else if (!strcasecmp(force_field, "EAM")){
749	+	ffCase = FF_EAM;
750	+	}
751	+	else if (!strcasecmp(force_field, "WATER")){
752	+	ffCase = FF_H2O;
753	+	}
754	+	else{
755	+	sprintf(painCave.errMsg, "SimSetup Error. Unrecognized force field -> %s\n",
756	+	force_field);
757	+	painCave.isFatal = 1;
758	+	simError();
759	+	}
760
761	<	#ifdef IS_MPI
949	<	sprintf( checkPointMsg,
950	<	"Successfully created the bends list.\n" );
951	<	MPIcheckPoint();
952	<	#endif // is_mpi
953	<
761	>	// get the ensemble
762
763	<	the_ff->initializeBends( the_bends );
956	<	}
763	>	strcpy(ensemble, globals->getEnsemble());
764
765	<	void SimSetup::makeTorsions( void ){
765	>	if (!strcasecmp(ensemble, "NVE")){
766	>	ensembleCase = NVE_ENS;
767	>	}
768	>	else if (!strcasecmp(ensemble, "NVT")){
769	>	ensembleCase = NVT_ENS;
770	>	}
771	>	else if (!strcasecmp(ensemble, "NPTi") || !strcasecmp(ensemble, "NPT")){
772	>	ensembleCase = NPTi_ENS;
773	>	}
774	>	else if (!strcasecmp(ensemble, "NPTf")){
775	>	ensembleCase = NPTf_ENS;
776	>	}
777	>	else if (!strcasecmp(ensemble, "NPTxyz")){
778	>	ensembleCase = NPTxyz_ENS;
779	>	}
780	>	else{
781	>	sprintf(painCave.errMsg,
782	>	"SimSetup Warning. Unrecognized Ensemble -> %s \n"
783	>	"\treverting to NVE for this simulation.\n",
784	>	ensemble);
785	>	painCave.isFatal = 0;
786	>	simError();
787	>	strcpy(ensemble, "NVE");
788	>	ensembleCase = NVE_ENS;
789	>	}
790
791	<	int i, j, k, index, offset, molIndex, exI, exJ, tempEx;
792	<	torsion_set* the_torsions;
962	<	TorsionStamp* current_torsion;
791	>	for (i = 0; i < nInfo; i++){
792	>	strcpy(info[i].ensemble, ensemble);
793
794	<	the_torsions = new torsion_set[tot_torsions];
965	<	index = 0;
966	<	offset = 0;
967	<	molIndex = 0;
968	<	for( i=0; i<n_components; i++ ){
794	>	// get the mixing rule
795
796	<	for( j=0; j<components_nmol[i]; j++ ){
796	>	strcpy(info[i].mixingRule, globals->getMixingRule());
797	>	info[i].usePBC = globals->getPBC();
798	>	}
799
800	<	#ifdef IS_MPI
973	<	if( mpiSim->getMyMolStart() <= molIndex &&
974	<	molIndex <= mpiSim->getMyMolEnd() ){
975	<	#endif // is_mpi
800	>	// get the components and calculate the tot_nMol and indvidual n_mol
801
802	<	for( k=0; k<comp_stamps[i]->getNTorsions(); k++ ){
802	>	the_components = globals->getComponents();
803	>	components_nmol = new int[n_components];
804
979	–	current_torsion = comp_stamps[i]->getTorsion( k );
980	–	the_torsions[index].a = current_torsion->getA() + offset;
981	–	the_torsions[index].b = current_torsion->getB() + offset;
982	–	the_torsions[index].c = current_torsion->getC() + offset;
983	–	the_torsions[index].d = current_torsion->getD() + offset;
805
806	<	exI = the_torsions[index].a;
807	<	exJ = the_torsions[index].d;
806	>	if (!globals->haveNMol()){
807	>	// we don't have the total number of molecules, so we assume it is
808	>	// given in each component
809
810	<
811	<	// exclude_I must always be the smaller of the pair
812	<	if( exI > exJ ){
813	<	tempEx = exI;
814	<	exI = exJ;
815	<	exJ = tempEx;
816	<	}
817	<
818	<
819	<	#ifdef IS_MPI
820	<
821	<	the_excludes[(index + tot_bonds + tot_bends)*2] =
822	<	the_atoms[exI]->getGlobalIndex() + 1;
1001	<	the_excludes[(index + tot_bonds + tot_bends)*2 + 1] =
1002	<	the_atoms[exJ]->getGlobalIndex() + 1;
1003	<
1004	<	#else  // isn't MPI
1005	<
1006	<	the_excludes[(index + tot_bonds + tot_bends)*2] =     exI + 1;
1007	<	the_excludes[(index + tot_bonds + tot_bends)*2 + 1] = exJ + 1;
1008	<	// fortran indexes from 1 (hence the +1 in the indexing)
1009	<	#endif  //is_mpi
1010	<
1011	<
1012	<	// increment the index and repeat;
1013	<	index++;
1014	<	}
1015	<	offset += comp_stamps[i]->getNAtoms();
1016	<
1017	<	#ifdef IS_MPI
1018	<	}
1019	<	#endif //is_mpi
1020	<
1021	<	molIndex++;
810	>	tot_nmol = 0;
811	>	for (i = 0; i < n_components; i++){
812	>	if (!the_components[i]->haveNMol()){
813	>	// we have a problem
814	>	sprintf(painCave.errMsg,
815	>	"SimSetup Error. No global NMol or component NMol given.\n"
816	>	"\tCannot calculate the number of atoms.\n");
817	>	painCave.isFatal = 1;
818	>	simError();
819	>	}
820	>
821	>	tot_nmol += the_components[i]->getNMol();
822	>	components_nmol[i] = the_components[i]->getNMol();
823		}
824		}
825	+	else{
826	+	sprintf(painCave.errMsg,
827	+	"SimSetup error.\n"
828	+	"\tSorry, the ability to specify total"
829	+	" nMols and then give molfractions in the components\n"
830	+	"\tis not currently supported."
831	+	" Please give nMol in the components.\n");
832	+	painCave.isFatal = 1;
833	+	simError();
834	+	}
835
836	<	the_ff->initializeTorsions( the_torsions );
837	<	}
836	>	//check whether sample time, status time, thermal time and reset time are divisble by dt
837	>	if (globals->haveSampleTime() && !isDivisible(globals->getSampleTime(), globals->getDt())){
838	>	sprintf(painCave.errMsg,
839	>	"Sample time is not divisible by dt.\n"
840	>	"\tThis will result in samples that are not uniformly\n"
841	>	"\tdistributed in time.  If this is a problem, change\n"
842	>	"\tyour sampleTime variable.\n");
843	>	painCave.isFatal = 0;
844	>	simError();
845	>	}
846
847	<	void SimSetup::initFromBass( void ){
847	>	if (globals->haveStatusTime() && !isDivisible(globals->getStatusTime(), globals->getDt())){
848	>	sprintf(painCave.errMsg,
849	>	"Status time is not divisible by dt.\n"
850	>	"\tThis will result in status reports that are not uniformly\n"
851	>	"\tdistributed in time.  If this is a problem, change \n"
852	>	"\tyour statusTime variable.\n");
853	>	painCave.isFatal = 0;
854	>	simError();
855	>	}
856
857	<	int i, j, k;
858	<	int n_cells;
859	<	double cellx, celly, cellz;
860	<	double temp1, temp2, temp3;
861	<	int n_per_extra;
862	<	int n_extra;
863	<	int have_extra, done;
857	>	if (globals->haveThermalTime() && !isDivisible(globals->getThermalTime(), globals->getDt())){
858	>	sprintf(painCave.errMsg,
859	>	"Thermal time is not divisible by dt.\n"
860	>	"\tThis will result in thermalizations that are not uniformly\n"
861	>	"\tdistributed in time.  If this is a problem, change \n"
862	>	"\tyour thermalTime variable.\n");
863	>	painCave.isFatal = 0;
864	>	simError();
865	>	}
866
867	<	temp1 = (double)tot_nmol / 4.0;
868	<	temp2 = pow( temp1, ( 1.0 / 3.0 ) );
869	<	temp3 = ceil( temp2 );
867	>	if (globals->haveResetTime() && !isDivisible(globals->getResetTime(), globals->getDt())){
868	>	sprintf(painCave.errMsg,
869	>	"Reset time is not divisible by dt.\n"
870	>	"\tThis will result in integrator resets that are not uniformly\n"
871	>	"\tdistributed in time.  If this is a problem, change\n"
872	>	"\tyour resetTime variable.\n");
873	>	painCave.isFatal = 0;
874	>	simError();
875	>	}
876
877	<	have_extra =0;
1043	<	if( temp2 < temp3 ){ // we have a non-complete lattice
1044	<	have_extra =1;
877	>	// set the status, sample, and thermal kick times
878
879	<	n_cells = (int)temp3 - 1;
880	<	cellx = simnfo->box_x / temp3;
881	<	celly = simnfo->box_y / temp3;
882	<	cellz = simnfo->box_z / temp3;
883	<	n_extra = tot_nmol - ( 4 * n_cells * n_cells * n_cells );
884	<	temp1 = ((double)n_extra) / ( pow( temp3, 3.0 ) - pow( n_cells, 3.0 ) );
885	<	n_per_extra = (int)ceil( temp1 );
879	>	for (i = 0; i < nInfo; i++){
880	>	if (globals->haveSampleTime()){
881	>	info[i].sampleTime = globals->getSampleTime();
882	>	info[i].statusTime = info[i].sampleTime;
883	>	}
884	>	else{
885	>	info[i].sampleTime = globals->getRunTime();
886	>	info[i].statusTime = info[i].sampleTime;
887	>	}
888
889	<	if( n_per_extra > 4){
890	<	sprintf( painCave.errMsg,
1056	<	"SimSetup error. There has been an error in constructing"
1057	<	" the non-complete lattice.\n" );
1058	<	painCave.isFatal = 1;
1059	<	simError();
889	>	if (globals->haveStatusTime()){
890	>	info[i].statusTime = globals->getStatusTime();
891		}
1061	–	}
1062	–	else{
1063	–	n_cells = (int)temp3;
1064	–	cellx = simnfo->box_x / temp3;
1065	–	celly = simnfo->box_y / temp3;
1066	–	cellz = simnfo->box_z / temp3;
1067	–	}
892
893	<	current_mol = 0;
894	<	current_comp_mol = 0;
895	<	current_comp = 0;
896	<	current_atom_ndx = 0;
893	>	if (globals->haveThermalTime()){
894	>	info[i].thermalTime = globals->getThermalTime();
895	>	} else {
896	>	info[i].thermalTime = globals->getRunTime();
897	>	}
898
899	<	for( i=0; i < n_cells ; i++ ){
900	<	for( j=0; j < n_cells; j++ ){
901	<	for( k=0; k < n_cells; k++ ){
899	>	info[i].resetIntegrator = 0;
900	>	if( globals->haveResetTime() ){
901	>	info[i].resetTime = globals->getResetTime();
902	>	info[i].resetIntegrator = 1;
903	>	}
904
905	<	makeElement( i * cellx,
906	<	j * celly,
907	<	k * cellz );
905	>	// check for the temperature set flag
906	>
907	>	if (globals->haveTempSet())
908	>	info[i].setTemp = globals->getTempSet();
909
910	<	makeElement( i * cellx + 0.5 * cellx,
1083	<	j * celly + 0.5 * celly,
1084	<	k * cellz );
910	>	// check for the extended State init
911
912	<	makeElement( i * cellx,
913	<	j * celly + 0.5 * celly,
914	<	k * cellz + 0.5 * cellz );
912	>	info[i].useInitXSstate = globals->getUseInitXSstate();
913	>	info[i].orthoTolerance = globals->getOrthoBoxTolerance();
914	>	info[i].useMolecularCutoffs = globals->getUseMolecularCutoffs();
915
916	<	makeElement( i * cellx + 0.5 * cellx,
917	<	j * celly,
918	<	k * cellz + 0.5 * cellz );
916	>
917	>	}
918	>
919	>	//setup seed for random number generator
920	>	int seedValue;
921	>
922	>	if (globals->haveSeed()){
923	>	seedValue = globals->getSeed();
924	>
925	>	if(seedValue / 1E9 == 0){
926	>	sprintf(painCave.errMsg,
927	>	"Seed for sprng library should contain at least 9 digits\n"
928	>	"OOPSE will generate a seed for user\n");
929	>	painCave.isFatal = 0;
930	>	simError();
931	>
932	>	//using seed generated by system instead of invalid seed set by user
933	>	#ifndef IS_MPI
934	>	seedValue = make_sprng_seed();
935	>	#else
936	>	if (worldRank == 0){
937	>	seedValue = make_sprng_seed();
938		}
939	+	MPI_Bcast(&seedValue, 1, MPI_INT, 0, MPI_COMM_WORLD);
940	+	#endif
941		}
942	+	}//end of if branch of globals->haveSeed()
943	+	else{
944	+
945	+	#ifndef IS_MPI
946	+	seedValue = make_sprng_seed();
947	+	#else
948	+	if (worldRank == 0){
949	+	seedValue = make_sprng_seed();
950	+	}
951	+	MPI_Bcast(&seedValue, 1, MPI_INT, 0, MPI_COMM_WORLD);
952	+	#endif
953	+	}//end of globals->haveSeed()
954	+
955	+	for (int i = 0; i < nInfo; i++){
956	+	info[i].setSeed(seedValue);
957		}
958	+
959	+	#ifdef IS_MPI
960	+	strcpy(checkPointMsg, "Successfully gathered all information from Bass\n");
961	+	MPIcheckPoint();
962	+	#endif // is_mpi
963	+	}
964
1097	–	if( have_extra ){
1098	–	done = 0;
965
966	<	int start_ndx;
967	<	for( i=0; i < (n_cells+1) && !done; i++ ){
968	<	for( j=0; j < (n_cells+1) && !done; j++ ){
966	>	void SimSetup::finalInfoCheck(void){
967	>	int index;
968	>	int usesDipoles;
969	>	int usesCharges;
970	>	int i;
971
972	<	if( i < n_cells ){
972	>	for (i = 0; i < nInfo; i++){
973	>	// check electrostatic parameters
974
975	<	if( j < n_cells ){
976	<	start_ndx = n_cells;
977	<	}
978	<	else start_ndx = 0;
979	<	}
980	<	else start_ndx = 0;
975	>	index = 0;
976	>	usesDipoles = 0;
977	>	while ((index < info[i].n_atoms) && !usesDipoles){
978	>	usesDipoles = (info[i].atoms[index])->hasDipole();
979	>	index++;
980	>	}
981	>	index = 0;
982	>	usesCharges = 0;
983	>	while ((index < info[i].n_atoms) && !usesCharges){
984	>	usesCharges= (info[i].atoms[index])->hasCharge();
985	>	index++;
986	>	}
987	>	#ifdef IS_MPI
988	>	int myUse = usesDipoles;
989	>	MPI_Allreduce(&myUse, &usesDipoles, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
990	>	#endif //is_mpi
991
992	<	for( k=start_ndx; k < (n_cells+1) && !done; k++ ){
992	>	double theEcr, theEst;
993
994	<	makeElement( i * cellx,
995	<	j * celly,
1117	<	k * cellz );
1118	<	done = ( current_mol >= tot_nmol );
994	>	if (globals->getUseRF()){
995	>	info[i].useReactionField = 1;
996
997	<	if( !done && n_per_extra > 1 ){
998	<	makeElement( i * cellx + 0.5 * cellx,
999	<	j * celly + 0.5 * celly,
1000	<	k * cellz );
1001	<	done = ( current_mol >= tot_nmol );
1002	<	}
997	>	if (!globals->haveECR()){
998	>	sprintf(painCave.errMsg,
999	>	"SimSetup Warning: No value was set for electrostaticCutoffRadius.\n"
1000	>	"\tOOPSE will use a default value of 15.0 angstroms"
1001	>	"\tfor the electrostaticCutoffRadius.\n");
1002	>	painCave.isFatal = 0;
1003	>	simError();
1004	>	theEcr = 15.0;
1005	>	}
1006	>	else{
1007	>	theEcr = globals->getECR();
1008	>	}
1009
1010	<	if( !done && n_per_extra > 2){
1011	<	makeElement( i * cellx,
1012	<	j * celly + 0.5 * celly,
1013	<	k * cellz + 0.5 * cellz );
1014	<	done = ( current_mol >= tot_nmol );
1015	<	}
1010	>	if (!globals->haveEST()){
1011	>	sprintf(painCave.errMsg,
1012	>	"SimSetup Warning: No value was set for electrostaticSkinThickness.\n"
1013	>	"\tOOPSE will use a default value of\n"
1014	>	"\t0.05 * electrostaticCutoffRadius\n"
1015	>	"\tfor the electrostaticSkinThickness\n");
1016	>	painCave.isFatal = 0;
1017	>	simError();
1018	>	theEst = 0.05 * theEcr;
1019	>	}
1020	>	else{
1021	>	theEst = globals->getEST();
1022	>	}
1023
1024	<	if( !done && n_per_extra > 3){
1025	<	makeElement( i * cellx + 0.5 * cellx,
1026	<	j * celly,
1027	<	k * cellz + 0.5 * cellz );
1028	<	done = ( current_mol >= tot_nmol );
1029	<	}
1030	<	}
1024	>	info[i].setDefaultEcr(theEcr, theEst);
1025	>
1026	>	if (!globals->haveDielectric()){
1027	>	sprintf(painCave.errMsg,
1028	>	"SimSetup Error: No Dielectric constant was set.\n"
1029	>	"\tYou are trying to use Reaction Field without"
1030	>	"\tsetting a dielectric constant!\n");
1031	>	painCave.isFatal = 1;
1032	>	simError();
1033		}
1034	+	info[i].dielectric = globals->getDielectric();
1035		}
1036	+	else{
1037	+	if (usesDipoles || usesCharges){
1038	+	if (!globals->haveECR()){
1039	+	sprintf(painCave.errMsg,
1040	+	"SimSetup Warning: No value was set for electrostaticCutoffRadius.\n"
1041	+	"\tOOPSE will use a default value of 15.0 angstroms"
1042	+	"\tfor the electrostaticCutoffRadius.\n");
1043	+	painCave.isFatal = 0;
1044	+	simError();
1045	+	theEcr = 15.0;
1046	+	}
1047	+	else{
1048	+	theEcr = globals->getECR();
1049	+	}
1050	+
1051	+	if (!globals->haveEST()){
1052	+	sprintf(painCave.errMsg,
1053	+	"SimSetup Warning: No value was set for electrostaticSkinThickness.\n"
1054	+	"\tOOPSE will use a default value of\n"
1055	+	"\t0.05 * electrostaticCutoffRadius\n"
1056	+	"\tfor the electrostaticSkinThickness\n");
1057	+	painCave.isFatal = 0;
1058	+	simError();
1059	+	theEst = 0.05 * theEcr;
1060	+	}
1061	+	else{
1062	+	theEst = globals->getEST();
1063	+	}
1064	+
1065	+	info[i].setDefaultEcr(theEcr, theEst);
1066	+	}
1067	+	}
1068		}
1069	+	#ifdef IS_MPI
1070	+	strcpy(checkPointMsg, "post processing checks out");
1071	+	MPIcheckPoint();
1072	+	#endif // is_mpi
1073	+	}
1074	+
1075	+	void SimSetup::initSystemCoords(void){
1076	+	int i;
1077
1078	+	char* inName;
1079
1080	<	for( i=0; i<simnfo->n_atoms; i++ ){
1081	<	simnfo->atoms[i]->set_vx( 0.0 );
1082	<	simnfo->atoms[i]->set_vy( 0.0 );
1083	<	simnfo->atoms[i]->set_vz( 0.0 );
1080	>	(info[0].getConfiguration())->createArrays(info[0].n_atoms);
1081	>
1082	>	for (i = 0; i < info[0].n_atoms; i++)
1083	>	info[0].atoms[i]->setCoords();
1084	>
1085	>	if (globals->haveInitialConfig()){
1086	>	InitializeFromFile* fileInit;
1087	>	#ifdef IS_MPI // is_mpi
1088	>	if (worldRank == 0){
1089	>	#endif //is_mpi
1090	>	inName = globals->getInitialConfig();
1091	>	fileInit = new InitializeFromFile(inName);
1092	>	#ifdef IS_MPI
1093	>	}
1094	>	else
1095	>	fileInit = new InitializeFromFile(NULL);
1096	>	#endif
1097	>	fileInit->readInit(info); // default velocities on
1098	>
1099	>	delete fileInit;
1100		}
1101	+	else{
1102	+
1103	+	// no init from bass
1104	+
1105	+	sprintf(painCave.errMsg,
1106	+	"Cannot intialize a simulation without an initial configuration file.\n");
1107	+	painCave.isFatal = 1;;
1108	+	simError();
1109	+
1110	+	}
1111	+
1112	+	#ifdef IS_MPI
1113	+	strcpy(checkPointMsg, "Successfully read in the initial configuration");
1114	+	MPIcheckPoint();
1115	+	#endif // is_mpi
1116		}
1117
1153	–	void SimSetup::makeElement( double x, double y, double z ){
1118
1119	+	void SimSetup::makeOutNames(void){
1120		int k;
1156	–	AtomStamp* current_atom;
1157	–	DirectionalAtom* dAtom;
1158	–	double rotMat[3][3];
1121
1160	–	for( k=0; k<comp_stamps[current_comp]->getNAtoms(); k++ ){
1122
1123	<	current_atom = comp_stamps[current_comp]->getAtom( k );
1124	<	if( !current_atom->havePosition() ){
1125	<	sprintf( painCave.errMsg,
1126	<	"SimSetup:initFromBass error.\n"
1127	<	"\tComponent %s, atom %s does not have a position specified.\n"
1128	<	"\tThe initialization routine is unable to give a start"
1129	<	" position.\n",
1130	<	comp_stamps[current_comp]->getID(),
1131	<	current_atom->getType() );
1123	>	for (k = 0; k < nInfo; k++){
1124	>	#ifdef IS_MPI
1125	>	if (worldRank == 0){
1126	>	#endif // is_mpi
1127	>
1128	>	if (globals->haveFinalConfig()){
1129	>	strcpy(info[k].finalName, globals->getFinalConfig());
1130	>	}
1131	>	else{
1132	>	strcpy(info[k].finalName, inFileName);
1133	>	char* endTest;
1134	>	int nameLength = strlen(info[k].finalName);
1135	>	endTest = &(info[k].finalName[nameLength - 5]);
1136	>	if (!strcmp(endTest, ".bass")){
1137	>	strcpy(endTest, ".eor");
1138	>	}
1139	>	else if (!strcmp(endTest, ".BASS")){
1140	>	strcpy(endTest, ".eor");
1141	>	}
1142	>	else{
1143	>	endTest = &(info[k].finalName[nameLength - 4]);
1144	>	if (!strcmp(endTest, ".bss")){
1145	>	strcpy(endTest, ".eor");
1146	>	}
1147	>	else if (!strcmp(endTest, ".mdl")){
1148	>	strcpy(endTest, ".eor");
1149	>	}
1150	>	else{
1151	>	strcat(info[k].finalName, ".eor");
1152	>	}
1153	>	}
1154	>	}
1155	>
1156	>	// make the sample and status out names
1157	>
1158	>	strcpy(info[k].sampleName, inFileName);
1159	>	char* endTest;
1160	>	int nameLength = strlen(info[k].sampleName);
1161	>	endTest = &(info[k].sampleName[nameLength - 5]);
1162	>	if (!strcmp(endTest, ".bass")){
1163	>	strcpy(endTest, ".dump");
1164	>	}
1165	>	else if (!strcmp(endTest, ".BASS")){
1166	>	strcpy(endTest, ".dump");
1167	>	}
1168	>	else{
1169	>	endTest = &(info[k].sampleName[nameLength - 4]);
1170	>	if (!strcmp(endTest, ".bss")){
1171	>	strcpy(endTest, ".dump");
1172	>	}
1173	>	else if (!strcmp(endTest, ".mdl")){
1174	>	strcpy(endTest, ".dump");
1175	>	}
1176	>	else{
1177	>	strcat(info[k].sampleName, ".dump");
1178	>	}
1179	>	}
1180	>
1181	>	strcpy(info[k].statusName, inFileName);
1182	>	nameLength = strlen(info[k].statusName);
1183	>	endTest = &(info[k].statusName[nameLength - 5]);
1184	>	if (!strcmp(endTest, ".bass")){
1185	>	strcpy(endTest, ".stat");
1186	>	}
1187	>	else if (!strcmp(endTest, ".BASS")){
1188	>	strcpy(endTest, ".stat");
1189	>	}
1190	>	else{
1191	>	endTest = &(info[k].statusName[nameLength - 4]);
1192	>	if (!strcmp(endTest, ".bss")){
1193	>	strcpy(endTest, ".stat");
1194	>	}
1195	>	else if (!strcmp(endTest, ".mdl")){
1196	>	strcpy(endTest, ".stat");
1197	>	}
1198	>	else{
1199	>	strcat(info[k].statusName, ".stat");
1200	>	}
1201	>	}
1202	>
1203	>	#ifdef IS_MPI
1204	>
1205	>	}
1206	>	#endif // is_mpi
1207	>	}
1208	>	}
1209	>
1210	>
1211	>	void SimSetup::sysObjectsCreation(void){
1212	>	int i, k;
1213	>
1214	>	// create the forceField
1215	>
1216	>	createFF();
1217	>
1218	>	// extract componentList
1219	>
1220	>	compList();
1221	>
1222	>	// calc the number of atoms, bond, bends, and torsions
1223	>
1224	>	calcSysValues();
1225	>
1226	>	#ifdef IS_MPI
1227	>	// divide the molecules among the processors
1228	>
1229	>	mpiMolDivide();
1230	>	#endif //is_mpi
1231	>
1232	>	// create the atom and SRI arrays. Also initialize Molecule Stamp ID's
1233	>
1234	>	makeSysArrays();
1235	>
1236	>	// make and initialize the molecules (all but atomic coordinates)
1237	>
1238	>	makeMolecules();
1239	>
1240	>	for (k = 0; k < nInfo; k++){
1241	>	info[k].identArray = new int[info[k].n_atoms];
1242	>	for (i = 0; i < info[k].n_atoms; i++){
1243	>	info[k].identArray[i] = info[k].atoms[i]->getIdent();
1244	>	}
1245	>	}
1246	>	}
1247	>
1248	>
1249	>	void SimSetup::createFF(void){
1250	>	switch (ffCase){
1251	>	case FF_DUFF:
1252	>	the_ff = new DUFF();
1253	>	break;
1254	>
1255	>	case FF_LJ:
1256	>	the_ff = new LJFF();
1257	>	break;
1258	>
1259	>	case FF_EAM:
1260	>	the_ff = new EAM_FF();
1261	>	break;
1262	>
1263	>	case FF_H2O:
1264	>	the_ff = new WATER();
1265	>	break;
1266	>
1267	>	default:
1268	>	sprintf(painCave.errMsg,
1269	>	"SimSetup Error. Unrecognized force field in case statement.\n");
1270		painCave.isFatal = 1;
1271		simError();
1272	+	}
1273	+
1274	+	#ifdef IS_MPI
1275	+	strcpy(checkPointMsg, "ForceField creation successful");
1276	+	MPIcheckPoint();
1277	+	#endif // is_mpi
1278	+	}
1279	+
1280	+
1281	+	void SimSetup::compList(void){
1282	+	int i;
1283	+	char* id;
1284	+	LinkedMolStamp* headStamp = new LinkedMolStamp();
1285	+	LinkedMolStamp* currentStamp = NULL;
1286	+	comp_stamps = new MoleculeStamp * [n_components];
1287	+
1288	+	// make an array of molecule stamps that match the components used.
1289	+	// also extract the used stamps out into a separate linked list
1290	+
1291	+	for (i = 0; i < nInfo; i++){
1292	+	info[i].nComponents = n_components;
1293	+	info[i].componentsNmol = components_nmol;
1294	+	info[i].compStamps = comp_stamps;
1295	+	info[i].headStamp = headStamp;
1296	+	}
1297	+
1298	+
1299	+	for (i = 0; i < n_components; i++){
1300	+	id = the_components[i]->getType();
1301	+	comp_stamps[i] = NULL;
1302	+
1303	+	// check to make sure the component isn't already in the list
1304	+
1305	+	comp_stamps[i] = headStamp->match(id);
1306	+	if (comp_stamps[i] == NULL){
1307	+	// extract the component from the list;
1308	+
1309	+	currentStamp = stamps->extractMolStamp(id);
1310	+	if (currentStamp == NULL){
1311	+	sprintf(painCave.errMsg,
1312	+	"SimSetup error: Component \"%s\" was not found in the "
1313	+	"list of declared molecules\n",
1314	+	id);
1315	+	painCave.isFatal = 1;
1316	+	simError();
1317	+	}
1318	+
1319	+	headStamp->add(currentStamp);
1320	+	comp_stamps[i] = headStamp->match(id);
1321		}
1322	+	}
1323
1324	<	the_atoms[current_atom_ndx]->setX( x + current_atom->getPosX() );
1325	<	the_atoms[current_atom_ndx]->setY( y + current_atom->getPosY() );
1326	<	the_atoms[current_atom_ndx]->setZ( z + current_atom->getPosZ() );
1324	>	#ifdef IS_MPI
1325	>	strcpy(checkPointMsg, "Component stamps successfully extracted\n");
1326	>	MPIcheckPoint();
1327	>	#endif // is_mpi
1328	>	}
1329
1330	<	if( the_atoms[current_atom_ndx]->isDirectional() ){
1330	>	void SimSetup::calcSysValues(void){
1331	>	int i;
1332
1333	<	dAtom = (DirectionalAtom *)the_atoms[current_atom_ndx];
1333	>	int* molMembershipArray;
1334
1335	<	rotMat[0][0] = 1.0;
1336	<	rotMat[0][1] = 0.0;
1337	<	rotMat[0][2] = 0.0;
1335	>	tot_atoms = 0;
1336	>	tot_bonds = 0;
1337	>	tot_bends = 0;
1338	>	tot_torsions = 0;
1339	>	tot_rigid = 0;
1340	>	for (i = 0; i < n_components; i++){
1341	>	tot_atoms += components_nmol[i] * comp_stamps[i]->getNAtoms();
1342	>	tot_bonds += components_nmol[i] * comp_stamps[i]->getNBonds();
1343	>	tot_bends += components_nmol[i] * comp_stamps[i]->getNBends();
1344	>	tot_torsions += components_nmol[i] * comp_stamps[i]->getNTorsions();
1345	>	tot_rigid += components_nmol[i] * comp_stamps[i]->getNRigidBodies();
1346	>	}
1347	>
1348	>	tot_SRI = tot_bonds + tot_bends + tot_torsions;
1349	>	molMembershipArray = new int[tot_atoms];
1350
1351	<	rotMat[1][0] = 0.0;
1352	<	rotMat[1][1] = 1.0;
1353	<	rotMat[1][2] = 0.0;
1351	>	for (i = 0; i < nInfo; i++){
1352	>	info[i].n_atoms = tot_atoms;
1353	>	info[i].n_bonds = tot_bonds;
1354	>	info[i].n_bends = tot_bends;
1355	>	info[i].n_torsions = tot_torsions;
1356	>	info[i].n_SRI = tot_SRI;
1357	>	info[i].n_mol = tot_nmol;
1358
1359	<	rotMat[2][0] = 0.0;
1360	<	rotMat[2][1] = 0.0;
1361	<	rotMat[2][2] = 1.0;
1359	>	info[i].molMembershipArray = molMembershipArray;
1360	>	}
1361	>	}
1362
1363	<	dAtom->setA( rotMat );
1363	>	#ifdef IS_MPI
1364	>
1365	>	void SimSetup::mpiMolDivide(void){
1366	>	int i, j, k;
1367	>	int localMol, allMol;
1368	>	int local_atoms, local_bonds, local_bends, local_torsions, local_SRI;
1369	>	int local_rigid;
1370	>	vector<int> globalMolIndex;
1371	>
1372	>	mpiSim = new mpiSimulation(info);
1373	>
1374	>	mpiSim->divideLabor();
1375	>	globalAtomIndex = mpiSim->getGlobalAtomIndex();
1376	>	//globalMolIndex = mpiSim->getGlobalMolIndex();
1377	>
1378	>	// set up the local variables
1379	>
1380	>	mol2proc = mpiSim->getMolToProcMap();
1381	>	molCompType = mpiSim->getMolComponentType();
1382	>
1383	>	allMol = 0;
1384	>	localMol = 0;
1385	>	local_atoms = 0;
1386	>	local_bonds = 0;
1387	>	local_bends = 0;
1388	>	local_torsions = 0;
1389	>	local_rigid = 0;
1390	>	globalAtomCounter = 0;
1391	>
1392	>	for (i = 0; i < n_components; i++){
1393	>	for (j = 0; j < components_nmol[i]; j++){
1394	>	if (mol2proc[allMol] == worldRank){
1395	>	local_atoms += comp_stamps[i]->getNAtoms();
1396	>	local_bonds += comp_stamps[i]->getNBonds();
1397	>	local_bends += comp_stamps[i]->getNBends();
1398	>	local_torsions += comp_stamps[i]->getNTorsions();
1399	>	local_rigid += comp_stamps[i]->getNRigidBodies();
1400	>	localMol++;
1401	>	}
1402	>	for (k = 0; k < comp_stamps[i]->getNAtoms(); k++){
1403	>	info[0].molMembershipArray[globalAtomCounter] = allMol;
1404	>	globalAtomCounter++;
1405	>	}
1406	>
1407	>	allMol++;
1408		}
1409	+	}
1410	+	local_SRI = local_bonds + local_bends + local_torsions;
1411
1412	<	current_atom_ndx++;
1412	>	info[0].n_atoms = mpiSim->getMyNlocal();
1413	>
1414	>
1415	>	if (local_atoms != info[0].n_atoms){
1416	>	sprintf(painCave.errMsg,
1417	>	"SimSetup error: mpiSim's localAtom (%d) and SimSetup's\n"
1418	>	"\tlocalAtom (%d) are not equal.\n",
1419	>	info[0].n_atoms, local_atoms);
1420	>	painCave.isFatal = 1;
1421	>	simError();
1422		}
1423
1424	<	current_mol++;
1425	<	current_comp_mol++;
1424	>	info[0].n_bonds = local_bonds;
1425	>	info[0].n_bends = local_bends;
1426	>	info[0].n_torsions = local_torsions;
1427	>	info[0].n_SRI = local_SRI;
1428	>	info[0].n_mol = localMol;
1429
1430	<	if( current_comp_mol >= components_nmol[current_comp] ){
1430	>	strcpy(checkPointMsg, "Passed nlocal consistency check.");
1431	>	MPIcheckPoint();
1432	>	}
1433
1434	<	current_comp_mol = 0;
1435	<	current_comp++;
1434	>	#endif // is_mpi
1435	>
1436	>
1437	>	void SimSetup::makeSysArrays(void){
1438	>
1439	>	#ifndef IS_MPI
1440	>	int k, j;
1441	>	#endif // is_mpi
1442	>	int i, l;
1443	>
1444	>	Atom** the_atoms;
1445	>	Molecule* the_molecules;
1446	>
1447	>	for (l = 0; l < nInfo; l++){
1448	>	// create the atom and short range interaction arrays
1449	>
1450	>	the_atoms = new Atom * [info[l].n_atoms];
1451	>	the_molecules = new Molecule[info[l].n_mol];
1452	>	int molIndex;
1453	>
1454	>	// initialize the molecule's stampID's
1455	>
1456	>	#ifdef IS_MPI
1457	>
1458	>
1459	>	molIndex = 0;
1460	>	for (i = 0; i < mpiSim->getTotNmol(); i++){
1461	>	if (mol2proc[i] == worldRank){
1462	>	the_molecules[molIndex].setStampID(molCompType[i]);
1463	>	the_molecules[molIndex].setMyIndex(molIndex);
1464	>	the_molecules[molIndex].setGlobalIndex(i);
1465	>	molIndex++;
1466	>	}
1467	>	}
1468	>
1469	>	#else // is_mpi
1470	>
1471	>	molIndex = 0;
1472	>	globalAtomCounter = 0;
1473	>	for (i = 0; i < n_components; i++){
1474	>	for (j = 0; j < components_nmol[i]; j++){
1475	>	the_molecules[molIndex].setStampID(i);
1476	>	the_molecules[molIndex].setMyIndex(molIndex);
1477	>	the_molecules[molIndex].setGlobalIndex(molIndex);
1478	>	for (k = 0; k < comp_stamps[i]->getNAtoms(); k++){
1479	>	info[l].molMembershipArray[globalAtomCounter] = molIndex;
1480	>	globalAtomCounter++;
1481	>	}
1482	>	molIndex++;
1483	>	}
1484	>	}
1485	>
1486	>
1487	>	#endif // is_mpi
1488	>
1489	>	info[l].globalExcludes = new int;
1490	>	info[l].globalExcludes[0] = 0;
1491	>
1492	>	// set the arrays into the SimInfo object
1493	>
1494	>	info[l].atoms = the_atoms;
1495	>	info[l].molecules = the_molecules;
1496	>	info[l].nGlobalExcludes = 0;
1497	>
1498	>	the_ff->setSimInfo(info);
1499	>	}
1500	>	}
1501	>
1502	>	void SimSetup::makeIntegrator(void){
1503	>	int k;
1504	>
1505	>	NVE<RealIntegrator>* myNVE = NULL;
1506	>	NVT<RealIntegrator>* myNVT = NULL;
1507	>	NPTi<NPT<RealIntegrator> >* myNPTi = NULL;
1508	>	NPTf<NPT<RealIntegrator> >* myNPTf = NULL;
1509	>	NPTxyz<NPT<RealIntegrator> >* myNPTxyz = NULL;
1510	>
1511	>	for (k = 0; k < nInfo; k++){
1512	>	switch (ensembleCase){
1513	>	case NVE_ENS:
1514	>	if (globals->haveZconstraints()){
1515	>	setupZConstraint(info[k]);
1516	>	myNVE = new ZConstraint<NVE<RealIntegrator> >(&(info[k]), the_ff);
1517	>	}
1518	>	else{
1519	>	myNVE = new NVE<RealIntegrator>(&(info[k]), the_ff);
1520	>	}
1521	>
1522	>	info->the_integrator = myNVE;
1523	>	break;
1524	>
1525	>	case NVT_ENS:
1526	>	if (globals->haveZconstraints()){
1527	>	setupZConstraint(info[k]);
1528	>	myNVT = new ZConstraint<NVT<RealIntegrator> >(&(info[k]), the_ff);
1529	>	}
1530	>	else
1531	>	myNVT = new NVT<RealIntegrator>(&(info[k]), the_ff);
1532	>
1533	>	myNVT->setTargetTemp(globals->getTargetTemp());
1534	>
1535	>	if (globals->haveTauThermostat())
1536	>	myNVT->setTauThermostat(globals->getTauThermostat());
1537	>	else{
1538	>	sprintf(painCave.errMsg,
1539	>	"SimSetup error: If you use the NVT\n"
1540	>	"\tensemble, you must set tauThermostat.\n");
1541	>	painCave.isFatal = 1;
1542	>	simError();
1543	>	}
1544	>
1545	>	info->the_integrator = myNVT;
1546	>	break;
1547	>
1548	>	case NPTi_ENS:
1549	>	if (globals->haveZconstraints()){
1550	>	setupZConstraint(info[k]);
1551	>	myNPTi = new ZConstraint<NPTi<NPT <RealIntegrator> > >(&(info[k]), the_ff);
1552	>	}
1553	>	else
1554	>	myNPTi = new NPTi<NPT<RealIntegrator> >(&(info[k]), the_ff);
1555	>
1556	>	myNPTi->setTargetTemp(globals->getTargetTemp());
1557	>
1558	>	if (globals->haveTargetPressure())
1559	>	myNPTi->setTargetPressure(globals->getTargetPressure());
1560	>	else{
1561	>	sprintf(painCave.errMsg,
1562	>	"SimSetup error: If you use a constant pressure\n"
1563	>	"\tensemble, you must set targetPressure in the BASS file.\n");
1564	>	painCave.isFatal = 1;
1565	>	simError();
1566	>	}
1567	>
1568	>	if (globals->haveTauThermostat())
1569	>	myNPTi->setTauThermostat(globals->getTauThermostat());
1570	>	else{
1571	>	sprintf(painCave.errMsg,
1572	>	"SimSetup error: If you use an NPT\n"
1573	>	"\tensemble, you must set tauThermostat.\n");
1574	>	painCave.isFatal = 1;
1575	>	simError();
1576	>	}
1577	>
1578	>	if (globals->haveTauBarostat())
1579	>	myNPTi->setTauBarostat(globals->getTauBarostat());
1580	>	else{
1581	>	sprintf(painCave.errMsg,
1582	>	"SimSetup error: If you use an NPT\n"
1583	>	"\tensemble, you must set tauBarostat.\n");
1584	>	painCave.isFatal = 1;
1585	>	simError();
1586	>	}
1587	>
1588	>	info->the_integrator = myNPTi;
1589	>	break;
1590	>
1591	>	case NPTf_ENS:
1592	>	if (globals->haveZconstraints()){
1593	>	setupZConstraint(info[k]);
1594	>	myNPTf = new ZConstraint<NPTf<NPT <RealIntegrator> > >(&(info[k]), the_ff);
1595	>	}
1596	>	else
1597	>	myNPTf = new NPTf<NPT <RealIntegrator> >(&(info[k]), the_ff);
1598	>
1599	>	myNPTf->setTargetTemp(globals->getTargetTemp());
1600	>
1601	>	if (globals->haveTargetPressure())
1602	>	myNPTf->setTargetPressure(globals->getTargetPressure());
1603	>	else{
1604	>	sprintf(painCave.errMsg,
1605	>	"SimSetup error: If you use a constant pressure\n"
1606	>	"\tensemble, you must set targetPressure in the BASS file.\n");
1607	>	painCave.isFatal = 1;
1608	>	simError();
1609	>	}
1610	>
1611	>	if (globals->haveTauThermostat())
1612	>	myNPTf->setTauThermostat(globals->getTauThermostat());
1613	>
1614	>	else{
1615	>	sprintf(painCave.errMsg,
1616	>	"SimSetup error: If you use an NPT\n"
1617	>	"\tensemble, you must set tauThermostat.\n");
1618	>	painCave.isFatal = 1;
1619	>	simError();
1620	>	}
1621	>
1622	>	if (globals->haveTauBarostat())
1623	>	myNPTf->setTauBarostat(globals->getTauBarostat());
1624	>
1625	>	else{
1626	>	sprintf(painCave.errMsg,
1627	>	"SimSetup error: If you use an NPT\n"
1628	>	"\tensemble, you must set tauBarostat.\n");
1629	>	painCave.isFatal = 1;
1630	>	simError();
1631	>	}
1632	>
1633	>	info->the_integrator = myNPTf;
1634	>	break;
1635	>
1636	>	case NPTxyz_ENS:
1637	>	if (globals->haveZconstraints()){
1638	>	setupZConstraint(info[k]);
1639	>	myNPTxyz = new ZConstraint<NPTxyz<NPT <RealIntegrator> > >(&(info[k]), the_ff);
1640	>	}
1641	>	else
1642	>	myNPTxyz = new NPTxyz<NPT <RealIntegrator> >(&(info[k]), the_ff);
1643	>
1644	>	myNPTxyz->setTargetTemp(globals->getTargetTemp());
1645	>
1646	>	if (globals->haveTargetPressure())
1647	>	myNPTxyz->setTargetPressure(globals->getTargetPressure());
1648	>	else{
1649	>	sprintf(painCave.errMsg,
1650	>	"SimSetup error: If you use a constant pressure\n"
1651	>	"\tensemble, you must set targetPressure in the BASS file.\n");
1652	>	painCave.isFatal = 1;
1653	>	simError();
1654	>	}
1655	>
1656	>	if (globals->haveTauThermostat())
1657	>	myNPTxyz->setTauThermostat(globals->getTauThermostat());
1658	>	else{
1659	>	sprintf(painCave.errMsg,
1660	>	"SimSetup error: If you use an NPT\n"
1661	>	"\tensemble, you must set tauThermostat.\n");
1662	>	painCave.isFatal = 1;
1663	>	simError();
1664	>	}
1665	>
1666	>	if (globals->haveTauBarostat())
1667	>	myNPTxyz->setTauBarostat(globals->getTauBarostat());
1668	>	else{
1669	>	sprintf(painCave.errMsg,
1670	>	"SimSetup error: If you use an NPT\n"
1671	>	"\tensemble, you must set tauBarostat.\n");
1672	>	painCave.isFatal = 1;
1673	>	simError();
1674	>	}
1675	>
1676	>	info->the_integrator = myNPTxyz;
1677	>	break;
1678	>
1679	>	default:
1680	>	sprintf(painCave.errMsg,
1681	>	"SimSetup Error. Unrecognized ensemble in case statement.\n");
1682	>	painCave.isFatal = 1;
1683	>	simError();
1684	>	}
1685		}
1686		}
1687	+
1688	+	void SimSetup::initFortran(void){
1689	+	info[0].refreshSim();
1690	+
1691	+	if (!strcmp(info[0].mixingRule, "standard")){
1692	+	the_ff->initForceField(LB_MIXING_RULE);
1693	+	}
1694	+	else if (!strcmp(info[0].mixingRule, "explicit")){
1695	+	the_ff->initForceField(EXPLICIT_MIXING_RULE);
1696	+	}
1697	+	else{
1698	+	sprintf(painCave.errMsg, "SimSetup Error: unknown mixing rule -> \"%s\"\n",
1699	+	info[0].mixingRule);
1700	+	painCave.isFatal = 1;
1701	+	simError();
1702	+	}
1703	+
1704	+
1705	+	#ifdef IS_MPI
1706	+	strcpy(checkPointMsg, "Successfully intialized the mixingRule for Fortran.");
1707	+	MPIcheckPoint();
1708	+	#endif // is_mpi
1709	+	}
1710	+
1711	+	void SimSetup::setupZConstraint(SimInfo& theInfo){
1712	+	int nZConstraints;
1713	+	ZconStamp** zconStamp;
1714	+
1715	+	if (globals->haveZconstraintTime()){
1716	+	//add sample time of z-constraint  into SimInfo's property list
1717	+	DoubleData* zconsTimeProp = new DoubleData();
1718	+	zconsTimeProp->setID(ZCONSTIME_ID);
1719	+	zconsTimeProp->setData(globals->getZconsTime());
1720	+	theInfo.addProperty(zconsTimeProp);
1721	+	}
1722	+	else{
1723	+	sprintf(painCave.errMsg,
1724	+	"ZConstraint error: If you use a ZConstraint,\n"
1725	+	"\tyou must set zconsTime.\n");
1726	+	painCave.isFatal = 1;
1727	+	simError();
1728	+	}
1729	+
1730	+	//push zconsTol into siminfo, if user does not specify
1731	+	//value for zconsTol, a default value will be used
1732	+	DoubleData* zconsTol = new DoubleData();
1733	+	zconsTol->setID(ZCONSTOL_ID);
1734	+	if (globals->haveZconsTol()){
1735	+	zconsTol->setData(globals->getZconsTol());
1736	+	}
1737	+	else{
1738	+	double defaultZConsTol = 0.01;
1739	+	sprintf(painCave.errMsg,
1740	+	"ZConstraint Warning: Tolerance for z-constraint method is not specified.\n"
1741	+	"\tOOPSE will use a default value of %f.\n"
1742	+	"\tTo set the tolerance, use the zconsTol variable.\n",
1743	+	defaultZConsTol);
1744	+	painCave.isFatal = 0;
1745	+	simError();
1746	+
1747	+	zconsTol->setData(defaultZConsTol);
1748	+	}
1749	+	theInfo.addProperty(zconsTol);
1750	+
1751	+	//set Force Subtraction Policy
1752	+	StringData* zconsForcePolicy = new StringData();
1753	+	zconsForcePolicy->setID(ZCONSFORCEPOLICY_ID);
1754	+
1755	+	if (globals->haveZconsForcePolicy()){
1756	+	zconsForcePolicy->setData(globals->getZconsForcePolicy());
1757	+	}
1758	+	else{
1759	+	sprintf(painCave.errMsg,
1760	+	"ZConstraint Warning: No force subtraction policy was set.\n"
1761	+	"\tOOPSE will use PolicyByMass.\n"
1762	+	"\tTo set the policy, use the zconsForcePolicy variable.\n");
1763	+	painCave.isFatal = 0;
1764	+	simError();
1765	+	zconsForcePolicy->setData("BYMASS");
1766	+	}
1767	+
1768	+	theInfo.addProperty(zconsForcePolicy);
1769	+
1770	+	//set zcons gap
1771	+	DoubleData* zconsGap = new DoubleData();
1772	+	zconsGap->setID(ZCONSGAP_ID);
1773	+
1774	+	if (globals->haveZConsGap()){
1775	+	zconsGap->setData(globals->getZconsGap());
1776	+	theInfo.addProperty(zconsGap);
1777	+	}
1778	+
1779	+	//set zcons fixtime
1780	+	DoubleData* zconsFixtime = new DoubleData();
1781	+	zconsFixtime->setID(ZCONSFIXTIME_ID);
1782	+
1783	+	if (globals->haveZConsFixTime()){
1784	+	zconsFixtime->setData(globals->getZconsFixtime());
1785	+	theInfo.addProperty(zconsFixtime);
1786	+	}
1787	+
1788	+	//set zconsUsingSMD
1789	+	IntData* zconsUsingSMD = new IntData();
1790	+	zconsUsingSMD->setID(ZCONSUSINGSMD_ID);
1791	+
1792	+	if (globals->haveZConsUsingSMD()){
1793	+	zconsUsingSMD->setData(globals->getZconsUsingSMD());
1794	+	theInfo.addProperty(zconsUsingSMD);
1795	+	}
1796	+
1797	+	//Determine the name of ouput file and add it into SimInfo's property list
1798	+	//Be careful, do not use inFileName, since it is a pointer which
1799	+	//point to a string at master node, and slave nodes do not contain that string
1800	+
1801	+	string zconsOutput(theInfo.finalName);
1802	+
1803	+	zconsOutput = zconsOutput.substr(0, zconsOutput.rfind(".")) + ".fz";
1804	+
1805	+	StringData* zconsFilename = new StringData();
1806	+	zconsFilename->setID(ZCONSFILENAME_ID);
1807	+	zconsFilename->setData(zconsOutput);
1808	+
1809	+	theInfo.addProperty(zconsFilename);
1810	+
1811	+	//setup index, pos and other parameters of z-constraint molecules
1812	+	nZConstraints = globals->getNzConstraints();
1813	+	theInfo.nZconstraints = nZConstraints;
1814	+
1815	+	zconStamp = globals->getZconStamp();
1816	+	ZConsParaItem tempParaItem;
1817	+
1818	+	ZConsParaData* zconsParaData = new ZConsParaData();
1819	+	zconsParaData->setID(ZCONSPARADATA_ID);
1820	+
1821	+	for (int i = 0; i < nZConstraints; i++){
1822	+	tempParaItem.havingZPos = zconStamp[i]->haveZpos();
1823	+	tempParaItem.zPos = zconStamp[i]->getZpos();
1824	+	tempParaItem.zconsIndex = zconStamp[i]->getMolIndex();
1825	+	tempParaItem.kRatio = zconStamp[i]->getKratio();
1826	+	tempParaItem.havingCantVel = zconStamp[i]->haveCantVel();
1827	+	tempParaItem.cantVel = zconStamp[i]->getCantVel();
1828	+	zconsParaData->addItem(tempParaItem);
1829	+	}
1830	+
1831	+	//check the uniqueness of index
1832	+	if(!zconsParaData->isIndexUnique()){
1833	+	sprintf(painCave.errMsg,
1834	+	"ZConstraint Error: molIndex is not unique!\n");
1835	+	painCave.isFatal = 1;
1836	+	simError();
1837	+	}
1838	+
1839	+	//sort the parameters by index of molecules
1840	+	zconsParaData->sortByIndex();
1841	+
1842	+	//push data into siminfo, therefore, we can retrieve later
1843	+	theInfo.addProperty(zconsParaData);
1844	+	}
1845	+
1846	+	void SimSetup::makeMinimizer(){
1847	+
1848	+	OOPSEMinimizer* myOOPSEMinimizer;
1849	+	MinimizerParameterSet* param;
1850	+	char minimizerName[100];
1851	+
1852	+	for (int i = 0; i < nInfo; i++){
1853	+
1854	+	//prepare parameter set for minimizer
1855	+	param = new MinimizerParameterSet();
1856	+	param->setDefaultParameter();
1857	+
1858	+	if (globals->haveMinimizer()){
1859	+	param->setFTol(globals->getMinFTol());
1860	+	}
1861	+
1862	+	if (globals->haveMinGTol()){
1863	+	param->setGTol(globals->getMinGTol());
1864	+	}
1865	+
1866	+	if (globals->haveMinMaxIter()){
1867	+	param->setMaxIteration(globals->getMinMaxIter());
1868	+	}
1869	+
1870	+	if (globals->haveMinWriteFrq()){
1871	+	param->setMaxIteration(globals->getMinMaxIter());
1872	+	}
1873	+
1874	+	if (globals->haveMinWriteFrq()){
1875	+	param->setWriteFrq(globals->getMinWriteFrq());
1876	+	}
1877	+
1878	+	if (globals->haveMinStepSize()){
1879	+	param->setStepSize(globals->getMinStepSize());
1880	+	}
1881	+
1882	+	if (globals->haveMinLSMaxIter()){
1883	+	param->setLineSearchMaxIteration(globals->getMinLSMaxIter());
1884	+	}
1885	+
1886	+	if (globals->haveMinLSTol()){
1887	+	param->setLineSearchTol(globals->getMinLSTol());
1888	+	}
1889	+
1890	+	strcpy(minimizerName, globals->getMinimizer());
1891	+
1892	+	if (!strcasecmp(minimizerName, "CG")){
1893	+	myOOPSEMinimizer = new PRCGMinimizer(&(info[i]), the_ff, param);
1894	+	}
1895	+	else if (!strcasecmp(minimizerName, "SD")){
1896	+	//myOOPSEMinimizer = MinimizerFactory.creatMinimizer("", &(info[i]), the_ff, param);
1897	+	myOOPSEMinimizer = new SDMinimizer(&(info[i]), the_ff, param);
1898	+	}
1899	+	else{
1900	+	sprintf(painCave.errMsg,
1901	+	"SimSetup error: Unrecognized Minimizer, use Conjugate Gradient \n");
1902	+	painCave.isFatal = 0;
1903	+	simError();
1904	+
1905	+	myOOPSEMinimizer = new PRCGMinimizer(&(info[i]), the_ff, param);
1906	+	}
1907	+	info[i].the_integrator = myOOPSEMinimizer;
1908	+
1909	+	//store the minimizer into simInfo
1910	+	info[i].the_minimizer = myOOPSEMinimizer;
1911	+	info[i].has_minimizer = true;
1912	+	}
1913	+
1914	+	}

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